@article {pmid39814778, year = {2025}, author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS}, title = {The Octocoral Trait Database: a global database of trait information for octocoral species.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {82}, pmid = {39814778}, issn = {2052-4463}, mesh = {*Anthozoa/classification ; Animals ; *Databases, Factual ; *Coral Reefs ; Biodiversity ; Ecosystem ; }, abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.}, }
@article {pmid39813953, year = {2025}, author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL}, title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.}, journal = {Environment international}, volume = {195}, number = {}, pages = {109260}, doi = {10.1016/j.envint.2025.109260}, pmid = {39813953}, issn = {1873-6750}, abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.}, }
@article {pmid39813347, year = {2025}, author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z}, title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq5038}, doi = {10.1126/sciadv.adq5038}, pmid = {39813347}, issn = {2375-2548}, mesh = {*Iron/metabolism ; *Siderophores/metabolism ; *Evolution, Molecular ; Ecosystem ; Pseudomonas/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Ligases/metabolism/genetics ; Humans ; Computational Biology/methods ; Bacterial Outer Membrane Proteins ; Receptors, Cell Surface ; }, abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.}, }
@article {pmid39809329, year = {2025}, author = {Amino, K and Hirakawa, T and Yago, M and Matsuo, T}, title = {Dorsoventral comparison of intraspecific variation in the butterfly wing pattern using a convolutional neural network.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240446}, doi = {10.1098/rsbl.2024.0446}, pmid = {39809329}, issn = {1744-957X}, support = {//ACT-X/ ; //Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Butterflies/anatomy & histology/genetics ; *Wings, Animal/anatomy & histology ; *Neural Networks, Computer ; *Sex Characteristics ; Male ; Female ; Species Specificity ; Biological Mimicry ; }, abstract = {Butterfly wing patterns exhibit notable differences between the dorsal and ventral surfaces, and morphological analyses of them have provided insights into the ecological and behavioural characteristics of wing patterns. Conventional methods for dorsoventral comparisons are constrained by the need for homologous patches or shared features between two surfaces, limiting their applicability across species. We used a convolutional neural network (CNN)-based analysis, which can compare images of the two surfaces without focusing on homologous patches or features, to detect dorsoventral bias in two types of intraspecific variation: sexual dimorphism and mimetic polymorphism. Using specimen images of 29 species, we first showed that the level of sexual dimorphism calculated by CNN-based analysis corresponded well with traditional assessments of sexual dissimilarity, demonstrating the validity of the method. Dorsal biases were widely detected in sexual dimorphism, suggesting that the conventional hypothesis of dorsally biased sexual selection can be supported in a broader range of species. In contrast, mimetic polymorphism showed no such bias, indicating the importance of both surfaces in mimicry. Our study demonstrates the potential versatility of CNN in comparing wing patterns between the two surfaces, while elucidating the relationship between dorsoventrally different selections and dorsoventral biases in intraspecific variations.}, }
@article {pmid39807382, year = {2024}, author = {Smith, SD and Geraghty, EM and Rivas, AL and Fasina, FO and Kosoy, M and Malania, L and Hoogesteijn, AL and Fair, JM}, title = {Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost-benefit oriented decision-making.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1492426}, pmid = {39807382}, issn = {2296-2565}, mesh = {Humans ; *Cost-Benefit Analysis ; *Decision Making ; Epidemiology/education ; Geographic Information Systems ; Learning ; }, abstract = {Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence-from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology-a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.}, }
@article {pmid39806613, year = {2024}, author = {Shen, A and Ye, J and Zhao, H and Qiang, W and Zhao, H and Huang, Y and Zhou, Y and Wang, Y and Li, X and Zhang, Z and Bian, J and Zhang, L and Wu, P and Wang, Y and Lu, Q}, title = {Risk factors and prediction model of breast cancer-related lymphoedema in a Chinese cancer centre: a prospective cohort study protocol.}, journal = {BMJ open}, volume = {14}, number = {12}, pages = {e089769}, doi = {10.1136/bmjopen-2024-089769}, pmid = {39806613}, issn = {2044-6055}, mesh = {Humans ; Female ; Prospective Studies ; China/epidemiology ; Risk Factors ; *Breast Neoplasms/complications/surgery ; *Breast Cancer Lymphedema/epidemiology/etiology ; Incidence ; Risk Assessment ; Middle Aged ; Adult ; Lymphedema/epidemiology/etiology ; Research Design ; East Asian People ; }, abstract = {INTRODUCTION: Lymphoedema is a distressing and long-term complication for breast cancer survivors. However, the reported incidence of lymphoedema varies, and its risk factors remain underexplored. Currently, a well-established risk prediction model is still lacking. This study aims to describe the rationale, objectives, protocol and baseline characteristics of a prospective cohort study focused on examining the incidence and risk factors of breast cancer-related lymphoedema (BCRL), as well as developing a risk prediction model.
METHODS AND ANALYSIS: This study is an ongoing single-centre prospective observational cohort study recruiting 1967 patients with breast cancer scheduled for surgery treatment in northern China between 15 February 2022 and 21 June 2023. Assessments will be conducted presurgery and at 1, 3, 6, 12, 18, 24, 30 and 36 months postsurgery. Bilateral limb circumferences will be measured by patients at home or by researchers at the outpatient clinics during follow-up visits. The diagnosis of lymphoedema is based on a relative limb volume increase of ≥10% from the preoperative assessment. Self-reported symptoms will be assessed to assist in diagnosis. Potential risk factors are classified into innate personal traits, behavioural lifestyle, interpersonal networks, socioeconomic status and macroenvironmental factors, based on health ecology model. Data collection, storage and management were conducted using the online 'H6WORLD' data management platform. Survival analysis using the Kaplan-Meier estimate will determine the incidence of BCRL. Risk factors of BCRL will be analysed using log-rank test and COX-LASSO regression. Traditional COX regression analysis and seven common survival analysis machine learning algorithms (COX, CARST, RSF, GBSM, XGBS, SSVM and SANN) will be employed for model construction and validation.
ETHICS AND DISSEMINATION: The study protocol was approved by the Biomedical Ethics Committee of Peking University (IRB00001052-21124) and the Research Ethics Committee of Tianjin Medical University Cancer Institute and Hospital (bc2023013). The results of this study will be published in peer-reviewed journals and will be presented at several research conferences.
TRIAL REGISTRATION NUMBER: ChiCTR2200057083.}, }
@article {pmid39671935, year = {2025}, author = {Paulukonis, EA and Purucker, ST}, title = {Spatiotemporally derived agricultural field delineations for species effects assessments and environmental decision support.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177967}, doi = {10.1016/j.scitotenv.2024.177967}, pmid = {39671935}, issn = {1879-1026}, mesh = {*Agriculture/methods ; *Environmental Monitoring/methods ; Crops, Agricultural ; Pesticides/analysis ; Risk Assessment/methods ; Decision Support Techniques ; United States ; Geographic Information Systems ; Ecosystem ; }, abstract = {Rural landscapes are strongly defined by the spatial distribution of agricultural fields. GIS layers that capture this information have much utility in many decision support contexts, particularly with regards to the intersection of agricultural pesticide use and endangered species habitat. The United States Department of Agriculture's Cropland Data Layer (CDL) is a georeferenced, annual resource that often serves a crucial role in pesticide risk-related decision support applications. However, CDL agriculture timeseries data are not mapped to explicit field boundaries, contributing to increased uncertainty regarding differentiated crop type spatial homogeneity and geographic extent, inherently adding complexity to multi-temporal crop monitoring and analyses efforts. We describe the development and testing of an approach for field delineation based on timeseries information from the 2008-2021 CDL at spatial scales relevant for endangered species risk assessment. We validate and test the approach against quantitative crop information and contextualize the outputs as part of a case study reconstructing past agricultural pesticide exposures to non-target species to demonstrate the utility of the method for ecological risk assessment decision support. The approach resulted in delineated field unit boundaries that effectively incorporated the unmodified CDL crop type generalized spatial distribution patterns; derived metrics closely corresponded with reported crop metrics for landscapes with proportionally significant agriculture use. When modified to reflect areas of mixed/small crop acreages, the method can provide a useful framework for large-scale field delineation of the CDL, which can complement ongoing environmental risk assessment and conservation efforts in agricultural landscapes.}, }
@article {pmid39584487, year = {2025}, author = {Daru, BH}, title = {A global database of butterfly species native distributions.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e4462}, doi = {10.1002/ecy.4462}, pmid = {39584487}, issn = {1939-9170}, support = {2345994//National Science Foundation/ ; 2416314//National Science Foundation/ ; }, mesh = {*Butterflies/physiology ; Animals ; *Animal Distribution ; Databases, Factual ; Species Specificity ; Ecosystem ; }, abstract = {Butterflies represent a diverse group of insects, playing key ecosystem roles such as pollination and their larval form engage in herbivory. Despite their importance, comprehensive global distribution data for butterfly species are lacking. This lack of comprehensive global data has hindered many large-scale questions in ecology, evolutionary biology, and conservation at the regional and global scales. Here, I use an integrative workflow that combines occurrence records, alpha hull polygons, species' dispersal capacity, and natural habitat and environmental variables within a framework of species distribution models to generate species-level native distributions for butterflies at a global scale in the contemporary period. The database releases native range maps for 10,372 extant species of butterflies at a spatial grain resolution of 5 arcmin (~10 km). This database has the potential to allow unprecedented large-scale analyses in ecology, biogeography, and conservation of butterflies. The maps are available in the WGS84 coordinate reference system (EPSG:4326 code) and stored as vector polygons in the GEOPACKAGE format for maximum compression, allowing easy data manipulation using a standard computer. I additionally provide each species' spatial raster. All maps and R scripts are open access and available for download in Dryad and Zenodo, respectively, and are guided by FAIR (Findable, Accessible, Interoperable, and Reusable) data principles. By making these data available to the scientific community, I aim to advance the sharing of biological data to stimulate more comprehensive research in ecology, biogeography, and conservation of butterflies.}, }
@article {pmid39805953, year = {2025}, author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C}, title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39805953}, issn = {2058-5276}, abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.}, }
@article {pmid39763978, year = {2024}, author = {Palma-Martínez, MJ and Posadas-García, YS and López-Ángeles, BE and Quiroz-López, C and Lewis, ACF and Bird, KA and Lasisi, T and Zaidi, AA and Sohail, M}, title = {The multi-scale complexity of human genetic variation beyond continental groups.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763978}, issn = {2692-8205}, support = {K99 HG012809/HG/NHGRI NIH HHS/United States ; R00 GM137076/GM/NIGMS NIH HHS/United States ; }, abstract = {Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings[1,2]. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups[3]. We introduce a network-based pipeline and visualization tool grounded in relational thinking[4], which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project[5], revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.}, }
@article {pmid39799926, year = {2025}, author = {Fridman, M and Krasko, O and Veyalkin, I}, title = {The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.}, journal = {Cancer epidemiology}, volume = {95}, number = {}, pages = {102745}, doi = {10.1016/j.canep.2025.102745}, pmid = {39799926}, issn = {1877-783X}, abstract = {BACKGROUND: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.
METHODS: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019. The incidence trends were analysed using Join-point regression software.
RESULTS: The highest peak of age-specific incidence curve was shown during the years 1980-2001 in the age group of 15-19 years old that was associated also with short-latency cases of post-Chernobyl PTC. This is the same age group that demonstrated significant growth of the incidence rate during the years 2006-2019, largely because of the increasing number of non-exposed patients with PTC (p < 0.001). Influence of post-Chernobyl exposure also can be seen in the young adults age-groups of patients (for 20-24 years old during the years 1980-2003 and 2013-2019, p < 0.001; for 25-29 years old during the years 1980-1999 and 1999-2011, p < 0.001).
CONCLUSION: After the Chernobyl accident, epidemiological waves that reflect the age shift of the group of children exposed to 131-I have consistently emerged. Currently, the incidence rate continues to increase only in the cohort of patients aged 20-44 years.}, }
@article {pmid39798660, year = {2025}, author = {Li, J and Lu, Y and Chen, X and Wang, L and Cao, Z and Lei, H and Zhang, Z and Wang, P and Sun, B}, title = {Seasonal variation of microbial community and diversity in the Taiwan Strait sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120809}, doi = {10.1016/j.envres.2025.120809}, pmid = {39798660}, issn = {1096-0953}, abstract = {Human activities and ocean currents in the Taiwan Strait exhibit significant seasonal variation, yet the response of marine microbes to ocean changes under anthropogenic and climatic stress remains unclear. Using 16S rRNA gene amplicon sequencing, we investigated the spatiotemporal dynamics and functional variations of microbial communities in sediment samples. Our findings revealed distinct seasonal patterns in microbial diversity and composition. Proteobacteria, Desulfobacterota, and Crenarchaeota dominated at the phylum level, while Candidatus Nitrosopumilus, Woeseia, and Subgroup 10 were prevalent at the genus level. Iron concentrations, heavy metals and C/N ratio were primary factors influencing microbial communities during specific seasons, whereas sulfur content, temperature fluctuations, and heavy metals shaped the entire microbial structure and diversity. Core microbial groups, including Desulfobulbus, Subgroup 10, Unidentified Latescibacterota, and Sumerlaea, played essential roles in regulating community structure and functional transitions. Marker species, such as Aliidiomarina sanyensis, Spirulina platensis, Croceimarina litoralis and Sulfuriflexus mobilis, acted as seasonal indicators. Bacteria exhibited survival strategy akin to higher organisms, encompassing process of synthesis, growth, dormancy, and disease resistance throughout the seasonal cycle. Core microbial groups and marker species in specific seasons can serve as indicators for monitoring and assessing the health of the Taiwan Strait ecosystem.}, }
@article {pmid39794649, year = {2025}, author = {Mohammad, L and Bandyopadhyay, J and Mondal, I and Altuwaijri, HA and Khatun, S and Hossain, SKA and Juliev, M}, title = {Assessing cropping system dynamics over three decades: remote sensing and GIS insights in Murshidabad-Jiaganj Block.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {164}, pmid = {39794649}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Remote Sensing Technology ; *Agriculture/methods ; *Geographic Information Systems ; Crops, Agricultural/growth & development ; Seasons ; }, abstract = {Agriculture is a significant contributor to the country's economic development. We used multiple Landsat images from 1990 to 2021 in the Murshidabad-Jiaganj Block to assess changes in the agricultural system and their underlying causes. The Rabi season saw a 10.99% growth in agrarian regions from 1990 to 2000 and an 8.86% increase in 2010, yet it declined by 28.12% in 2021. During the summer, the cultivated lands diminished by 26.63%, 19.43%, and 19.64%, while in the Kharif season, they declined by 21.78%, 15.68%, and 11.99% from 1990 in the years 2000, 2010, and 2021, respectively. The agricultural area had 36.82%, 34.16%, and 19.01% increases between 1990 and 2021, respectively. Regarding direction, farmland acreage decreased in all zones except the SSE, which had a 0.95% increase. Mono-, double-, and triple-cropping systems have decreased in area, while multi-cropping systems have experienced increases of 43.51%, 4.50%, and 18.49% in 1990-2021, respectively. The multi-cropping system has a good correlation with all agroclimatic factors. The reduction of irrigated lands post-2009 significantly affected the agriculture system. The fall in agricultural employment in recent decades is attributable to migration seeking higher-paying occupations. The advancement of accurate remote sensing-based modeling is crucial for mitigating food security risks, particularly those posed by climate change, and informing policy decisions.}, }
@article {pmid39794678, year = {2025}, author = {Sasia, I and Bueno, G and Etxano, I}, title = {Amalur EIS: a system for calculating the environmental impacts of industrial sites from E-PRTR records.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {163}, pmid = {39794678}, issn = {1573-2959}, support = {IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; IT 1567-22 Ekopol Research Group (UPV/EHU)//Department of Education of the Basque Government/ ; }, mesh = {*Environmental Monitoring/methods ; Climate Change ; Environment ; Europe ; Databases, Factual ; Industry ; Environmental Pollutants/analysis ; Environmental Pollution/statistics & numerical data ; }, abstract = {This article presents Amalur EIS (https://www.amalur-eis.eus/), an Environmental Information System that estimates environmental impacts using data sourced from the European Pollutant Release and Transfer Register database (E-PRTR). The system uses data on the releases into land, air and water of 31,556 European industrial facilities for the period 2007-2021. Amalur EIS calculates environmental impacts of industrial releases using 31 life cycle impact assessment methods (LCIA) and covering 78 of the 91 pollutants regulated by the PRTR Protocol. The system has been constructed using a two-layer software infrastructure: (i) a data layer supported by a relational database built in Postgres and (ii) a presentation layer built in Tableau, so it provides user-friendly access to the information. For an illustrative analysis of the tool, the EF 3.0 LCIA method recommended by the European Commission was used, including normalisation and weighting steps for a better comparison. The analysis concludes that the climate change impact category contributes the most (68.6%) to the total impacts, while the largest contributor from an economic activity perspective is the energy sector (59.5%). Geographically, both elements coincide in the German regions of Düsseldorf, Köln and Brandenburg, resulting in the concentration of the largest impacts at the European regional level. In fact, Germany is the country with the highest impact (20.3% of total). Beyond this analysis, Amalur EIS is poised to be a valuable tool for tracking the transition towards sustainability, particularly in Europe.}, }
@article {pmid39793033, year = {2025}, author = {Clauss, M and Roller, M and Bertelsen, MF and Rudolf von Rohr, C and Müller, DWH and Schiffmann, C and Kummrow, M and Encke, D and Ferreira, S and Duvall, ES and Maré, C and Abraham, AJ}, title = {Zoos must embrace animal death for education and conservation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {1}, pages = {e2414565121}, doi = {10.1073/pnas.2414565121}, pmid = {39793033}, issn = {1091-6490}, support = {101062339//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, }
@article {pmid39792995, year = {2025}, author = {Soeishi, T and Nakata, A and Nagata, T and Akutsu, S and Tondokoro, T and Inoue, Y and Katsumura, F and Kikunaga, K}, title = {Predicting depressive symptoms and psychological distress by circulating inflammatory mediators: A 16-month prospective study in Japanese white-collar employees.}, journal = {Journal of occupational and environmental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1097/JOM.0000000000003307}, pmid = {39792995}, issn = {1536-5948}, abstract = {OBJECTIVE: Although increasing evidence suggests that depression/distress involves inflammatory processes, its potential sex differences and the temporal directions for this association remain elusive.
METHODS: We examined the temporal association between serum inflammatory mediators and depression/distress as measured by the Center for Epidemiologic Studies Depression Scale (CES-D) and the Kessler Psychological Distress Scale (K6), in non-depressed working men and women (n = 61 and 43, respectively) by a 16-month prospective design.
RESULTS: Fully-adjusted partial correlation analyses revealed that in men, a lower IFN-γ predicted subsequent increases in CES-D and K6 scores, while a higher TNF-α predicted increased K6 scores. In women, a higher IFN-γ predicted a subsequent increase in the CES-D score. CES-D and K6 scores did not predict inflammatory mediators at follow-up.
CONCLUSIONS: The finding suggests that inflammatory activation precedes depression/distress with distinct sex differences.}, }
@article {pmid39792790, year = {2025}, author = {Kherroubi Garcia, I and Erdmann, C and Gesing, S and Barton, M and Cadwallader, L and Hengeveld, G and Kirkpatrick, CR and Knight, K and Lemmen, C and Ringuette, R and Zhan, Q and Harrison, M and Mac Gabhann, F and Meyers, N and Osborne, C and Till, C and Brenner, P and Buys, M and Chen, M and Lee, A and Papin, J and Rao, Y}, title = {Ten simple rules for good model-sharing practices.}, journal = {PLoS computational biology}, volume = {21}, number = {1}, pages = {e1012702}, doi = {10.1371/journal.pcbi.1012702}, pmid = {39792790}, issn = {1553-7358}, mesh = {*Information Dissemination/methods ; Humans ; *Computational Biology ; Computer Simulation ; }, abstract = {Computational models are complex scientific constructs that have become essential for us to better understand the world. Many models are valuable for peers within and beyond disciplinary boundaries. However, there are no widely agreed-upon standards for sharing models. This paper suggests 10 simple rules for you to both (i) ensure you share models in a way that is at least "good enough," and (ii) enable others to lead the change towards better model-sharing practices.}, }
@article {pmid39789290, year = {2025}, author = {Sağlam, S and Özdemir, E and Özden, Ö and Makineci, E and Özkan, UY and Bingöl, D and Güzelçimen, F}, title = {The effects of some chemical compounds on the sound absorbing ability of tree bark.}, journal = {Biologia futura}, volume = {}, number = {}, pages = {}, pmid = {39789290}, issn = {2676-8607}, abstract = {Tree bark is an important natural polymer for sound absorption. The main components in the bark of different tree species are polymers with high molecular weight such as cellulose, hemicellulose, and lignin. The aim of this study is to determine the noise reduction coefficient (NRC), lignin, alcohol-benzene solubility (ABS), carbon (C), and nitrogen (N) contents in samples taken from the bark of different tree species-black locust (Robinia pseudoacacia), narrow-leaved ash (Fraxinus angustifolia), stone pine (Pinus pinea), silver lime (Tilia tomentosa), sweet chestnut (Castanea sativa), sessile oak (Quercus petraea), and maritime pine (Pinus pinaster) and to investigate the relationship between these chemical properties and sound absorption measurements. Tree species showed a statistically significant difference in terms of all measured variables. In the correlation matrix obtained as a result of the analysis, only ABS showed a significant and the highest positive correlation with the NRC, with a correlation coefficient of r = 0.812. ABS in bark is seen as the most important chemical factor regarding sound retention, indicating the abundance of extractives in barks of different tree species. An investigation into the relationship between sound retention and different extractive substance and contents of different extractive substances in bark is recommended for further studies.}, }
@article {pmid39789035, year = {2025}, author = {Li, F and Xia, H and Miao, J and Yang, J}, title = {Changes of the ecological environment status in villages under the background of traditional village preservation: a case study in Enshi Tujia and Miao Autonomous Prefecture.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1504}, pmid = {39789035}, issn = {2045-2322}, support = {42271318//National Natural Science Foundation of China/ ; }, mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; China ; Humans ; Rural Population ; Geographic Information Systems ; }, abstract = {The preservation of Chinese traditional villages plays a crucial role in promoting the sustainable development of rural natural, cultural, and ecological environments. It is also a key strategy for achieving rural revitalization. Current research on traditional villages predominantly focuses on the realm of cultural landscapes, with an emphasis on preserving the cultural ecological value of these communities. In comparison, discussions on the quality of the ecological environment of villages from the perspectives of natural environment, economic environment, and the social organizational environment within regional development are relatively scarce. Our study employed GIS and RS technology and refers to the Technical Criterion for Ecosystem Status Evaluation. Several sub-indices of the ecological environment status, including the biological richness index, vegetation coverage index, water network density index, and land stress index, were selected to construct an ecological environment assessment model. This model was used to analyze the spatial-temporal changes in the ecological environment status of each county, county-level city, and traditional village within the jurisdiction of Enshi Tujia and Miao Autonomous Prefecture and its surrounding areas from 2010 to 2020. The study quantitatively evaluated the ecological environment status of each county, county-level city, and village in Enshi before and after the implementation of traditional village preservation policies. Through comparative analysis, the study revealed the impact of these policies on the natural ecological environment of the study area. The results indicated the following: (1) From 2010 to 2020, the ecological index (EI) values in the villages of Enshi Prefecture exhibited a similar trend to the EI values in the respective counties and county-level cities they are located in, although significant differences in magnitude of change were observed. (2) The EI values in the counties, county-level cities, and villages demonstrated greater variation in the latter five years of the decade (2015-2020) compared to the previous five years (2010-2015). (3) In 2020, the EI value of the villages experienced more significant changes compared to 2010, whereas the overall EI value of the counties and county-level cities showed less pronounced changes. The findings of this study suggest that the traditional village preservation policies implemented in Enshi Prefecture have both positive and negative impacts on the ecological environment of the surrounding areas of protected villages, and these impacts become increasingly evident over time. By comparing and analyzing the ecological changes in the surrounding areas of traditional villages in Enshi Prefecture with the overall ecological changes in the respective counties and county-level cities, our study employs quantitative analytical methods to delve into the impact of traditional village conservation policies on the natural ecological environment. It assesses the effects of policy implementation on the natural ecological environment of traditional villages, analyzing both the positive and negative impacts brought about by the execution of these policies, with the aim of effectively guiding the natural ecological conditions of traditional villages towards a more healthy trajectory of development.}, }
@article {pmid39788970, year = {2025}, author = {Sánchez-Jardón, L and Hernández de Diego, A and Mackenzie, R and Villodre, M and Arnaiz-Schmitz, C and Schmitz, MF and Acosta-Gallo, B}, title = {Bryophyte literature records database of Aysén, Chilean sub-Antarctic ecoregion.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {36}, pmid = {39788970}, issn = {2052-4463}, mesh = {*Bryophyta ; Chile ; *Biodiversity ; Antarctic Regions ; Ecosystem ; Databases, Factual ; }, abstract = {The Chilean sub-Antarctic ecoregion hosts the largest expanse of temperate forests, wetlands and peatlands, as well as the largest proportion of protected areas in the southern hemisphere. Bryophytes are highly diverse and ecologically essential in sub-Antarctic ecosystems and are considered as biodiversity loss indicators caused by the current socio-ecological crisis. However, knowledge about their biodiversity is rather limited. Integrating the available information on bryophyte diversity in regional platforms such as SIB-Aysén can be useful to acknowledge their ecological importance and remarkable biodiversity. This article integrates 345 records of 273 bryophyte taxa known in the region of Aysén and emphasizes the need to include citizen science as a tool to increase observations in lesser-known taxonomic groups.}, }
@article {pmid39787642, year = {2024}, author = {Aanes, H and Vigeland, MD and Star, B and Gilfillan, GD and Mattingsdal, M and Trøan, S and Strand, M and Eide, LM and Hanssen, EN}, title = {Heating up three cold cases in Norway using investigative genetic genealogy.}, journal = {Forensic science international. Genetics}, volume = {76}, number = {}, pages = {103217}, doi = {10.1016/j.fsigen.2024.103217}, pmid = {39787642}, issn = {1878-0326}, abstract = {With the advent of commercial DNA databases, investigative genetic genealogy (IGG) has emerged as a powerful forensic tool, rivalling the impact of STR analyses, introduced four decades ago. IGG has been frequently applied in the US and tested in other countries, but never in Norway. Here, we apply IGG to three cold criminal cases and successfully identify the donor of the DNA in two of these cases. Our findings suggest that when combined with phenotypic prediction and case information, IGG holds substantial potential for resolving both active and cold cases in Norway. This potential is amplified by the digitalization of archives and the transparent and structured nature of society in Norway. Additionally, the databases exhibit sufficient representation to yield matches with distant relatives. Moreover, this work has uncovered a series of lingering research questions spanning the entire workflow from DNA extraction to genealogy research. Finally, we highlight the possibility that more insights can be gleaned from genetic profiles, for instance using an accurate age prediction method. The results show that IGG can be successfully applied in Norway, having reached a level of maturity that enables identification of unknown individuals in cases where DNA is accessible.}, }
@article {pmid39787194, year = {2025}, author = {Bantie, GM and Tadege, M and Nigussie, TZ and Woya, AA and Tekile, AK and Melese, AA and Ayalew, S and Beyene, BB and Wubetu, GY}, title = {Regional disparities of full pentavalent vaccine uptake and the determinants in Ethiopia: Mapping and spatial analysis using the EDHS data.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0312514}, doi = {10.1371/journal.pone.0312514}, pmid = {39787194}, issn = {1932-6203}, mesh = {Humans ; Ethiopia ; Infant ; Female ; Adult ; *Spatial Analysis ; Male ; *Vaccination/statistics & numerical data ; Diphtheria-Tetanus-Pertussis Vaccine/administration & dosage ; Hepatitis B Vaccines/administration & dosage ; Young Adult ; Immunization Programs/statistics & numerical data ; Middle Aged ; Haemophilus Vaccines ; Adolescent ; Vaccination Coverage/statistics & numerical data ; Vaccines, Combined ; }, abstract = {BACKGROUND: The full pentavalent (DPT-HepB-Hib) vaccination is the main strategy to prevent five communicable diseases in early childhood, especially in countries with huge communicable disease burdens like Ethiopia. Exploring spatial distributions and determinants of full pentavalent vaccination status in minor ecological areas in Ethiopia is crucial for creating targeted immunization campaigns and monitoring the advancement of accomplishing sustainable development goals. This study aimed to investigate the spatial disparities and determinants of full pentavalent vaccination among 12-23-month-old children in Ethiopia.
METHOD: The data on pentavalent vaccine uptake was found in the Ethiopian Health and Demographic Survey (EDHS, 2019). A two-stage cluster sampling method was applied to collect the EDHS data. The enumeration area was the primary sample unit while the household served as the secondary sampling unit. The geographical variations of full pentavalent vaccine uptake were explored using Quantum Geographic Information System (QGIS) software. The significant predictors of full pentavalent vaccination were identified using a simple logistic regression model through R version 4.1 software.
RESULT: The national full pentavalent vaccine uptake was 59.2%. The spatial distribution of full pentavalent vaccine uptake was not uniform in Ethiopia. Spatial cluster analysis revealed that most of low coverage regions for full pentavalent vaccine uptake were Afar, Somali, and Harari. The regions with the highest and lowest rates of vaccine uptake were Tigray and Harari region, respectively. Maternal age of 35-49 years (AOR = 3.42; 95% CI: 1.99, 5.87), and 25-34 years (AOR = 1.55; 95% CI: 1.17, 2.19), primary education attended (AOR = 1.51; 95%CI: 1.07, 2.11), richness wealth index (AOR = 1.96; 95% CI: 1.40, 2.75), birth order of 1-3 (AOR = 1.88; 95% CI: 1.19, 2.96), and delivery in the health facility (AOR = 3.41: 95% CI: 2.52, 4.61) were the determinants of full pentavalent vaccine uptake in Ethiopia.
CONCLUSION: Ethiopia's full pentavalent vaccine uptake was far lower than the global target. Older maternal age, maternal education, wealth index, birth order, and giving birth in a health facility were the determinants of full pentavalent vaccine uptake. Special attention should be given to Afar, Somali, and Harari regions, to strengthen the vaccine uptake. Moreover, improved socioeconomic status and getting maternal health services during delivery are necessary to enhance vaccine uptake.}, }
@article {pmid39750058, year = {2024}, author = {Jain, S and Srinivasan, R and Helton, TJ and Karthikeyan, R}, title = {TXSELECT: a web-based decision support system for regional assessment of potential E. coli loads using a spatially explicit approach.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {59}, number = {10}, pages = {550-561}, doi = {10.1080/10934529.2024.2445953}, pmid = {39750058}, issn = {1532-4117}, mesh = {*Escherichia coli/isolation & purification ; Texas ; *Internet ; Environmental Monitoring/methods ; Water Microbiology ; Decision Support Techniques ; }, abstract = {Bacterial source characterization and allocation are imperative to watershed planning and identifying best management practices. The Spatially Explicit Load Enrichment Calculation Tool (SELECT) has been extensively utilized in watershed protection plans to evaluate the potential bacteria loads and sources in impaired watersheds. However, collecting data, compiling inputs, and spatially mapping sources can be arduous, time-intensive, expensive, and iterative until potential bacteria loads are appropriately allocated to sources based on stakeholder recommendations. We developed a web-based decision support system (DSS), TXSELECT (https://tx.select.tamu.edu), providing a user-friendly interface to run the SELECT model on Texas watersheds. The DSS includes pre-determined watershed-specific inputs that can be readily adjusted within the interface based on user preference and stakeholder recommendations, obviating the necessity for expensive GIS tools and data extraction. To illustrate the applications of TXSELECT, we implemented it in the entire coverage area to identify the potential hotspots and source contributions for Escherichia coli at a regional scale. Median potential E. coli loads were significantly higher in subwatersheds not supporting recreation use. Overall, the large-scale application of SELECT has the potential to aid in prioritizing management measures in watersheds that are less frequently monitored but could have an elevated risk of impairment.}, }
@article {pmid39560426, year = {2025}, author = {Zhu, H-H and Liu, M-M and Boekhout, T and Wang, Q-M}, title = {Improvement of a MALDI-TOF database for the reliable identification of Candidozyma auris (formally Candida auris) and related species.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0144424}, pmid = {39560426}, issn = {2165-0497}, mesh = {*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Humans ; *Candidiasis/microbiology/diagnosis ; Candida auris/chemistry/isolation & purification/classification ; Databases, Factual ; Mycological Typing Techniques/methods ; Candida/classification/isolation & purification/chemistry ; }, abstract = {UNLABELLED: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of Candidozyma auris (formerly known as Candida auris) and 11 species of the Candidozyma haemuli species complex, including C. chanthaburiensis, C. duobushaemuli, C. haemuli, C. heveicola, C. khanbhai, C. konsanensis, C. metrosideri, C. ohialehuae, C. pseudohaemuli, C. ruelliae, and C. vulturna. Seventy-one Candidozyma isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus Candidozyma, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify C. auris and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus Candidozyma in clinical practice.
IMPORTANCE: Importance Candidozyma auris, also known as Candida auris, has quickly spread across the world, and prompt identification of C. auris from infected individuals is critical. However, a standard identification method is lacking for the identification of C. auris in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all Candidozyma species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of Candidozyma can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of C. auris and related species of clinical importance and help the clinician to decide on early treatment.}, }
@article {pmid39304763, year = {2025}, author = {Pakkir Shah, AK and Walter, A and Ottosson, F and Russo, F and Navarro-Diaz, M and Boldt, J and Kalinski, JJ and Kontou, EE and Elofson, J and Polyzois, A and González-Marín, C and Farrell, S and Aggerbeck, MR and Pruksatrakul, T and Chan, N and Wang, Y and Pöchhacker, M and Brungs, C and Cámara, B and Caraballo-Rodríguez, AM and Cumsille, A and de Oliveira, F and Dührkop, K and El Abiead, Y and Geibel, C and Graves, LG and Hansen, M and Heuckeroth, S and Knoblauch, S and Kostenko, A and Kuijpers, MCM and Mildau, K and Papadopoulos Lambidis, S and Portal Gomes, PW and Schramm, T and Steuer-Lodd, K and Stincone, P and Tayyab, S and Vitale, GA and Wagner, BC and Xing, S and Yazzie, MT and Zuffa, S and de Kruijff, M and Beemelmanns, C and Link, H and Mayer, C and van der Hooft, JJJ and Damiani, T and Pluskal, T and Dorrestein, P and Stanstrup, J and Schmid, R and Wang, M and Aron, A and Ernst, M and Petras, D}, title = {Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.}, journal = {Nature protocols}, volume = {20}, number = {1}, pages = {92-162}, pmid = {39304763}, issn = {1750-2799}, support = {EXC 2124//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {*Metabolomics/methods ; Chromatography, Liquid/methods ; Software ; Tandem Mass Spectrometry/methods ; Data Interpretation, Statistical ; }, abstract = {Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices. Here we provide a comprehensive guide for the statistical analysis of FBMN results, focusing on the downstream analysis of the FBMN output table. We explain the data structure and principles of data cleanup and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. All code is shared in the form of Jupyter Notebooks (https://github.com/Functional-Metabolomics-Lab/FBMN-STATS). Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/) to lower the barrier of entry for new users and for educational purposes. Finally, we also show users how to integrate their statistical results into the molecular network using the Cytoscape visualization tool. Throughout the protocol, we use a previously published environmental metabolomics dataset for demonstration purposes. Together, the protocol, code and web application provide a complete guide and toolbox for FBMN data integration, cleanup and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking and can be easily adapted to other mass spectrometry feature detection, annotation and networking tools.}, }
@article {pmid39778451, year = {2025}, author = {Lausch, A and Selsam, P and Heege, T and von Trentini, F and Almeroth, A and Borg, E and Klenke, R and Bumberger, J}, title = {Monitoring and modelling landscape structure, land use intensity and landscape change as drivers of water quality using remote sensing.}, journal = {The Science of the total environment}, volume = {960}, number = {}, pages = {178347}, doi = {10.1016/j.scitotenv.2024.178347}, pmid = {39778451}, issn = {1879-1026}, abstract = {The interactions between landscape structure, land use intensity (LUI), climate change, and ecological processes significantly impact hydrological processes, affecting water quality. Monitoring these factors is crucial for understanding their influence on water quality. Remote sensing (RS) provides a continuous, standardized approach to capture landscape structures, LUI, and landscape changes over long-term time series. In this study, RS-based indicators from Landsat data (2018-2021) were used to assess landscape structure, LUI, and land use change for a study area in northern Germany, applying the ESIS/Imalys tool. These indicators were then used to model and predict water quality (Chla) in 119 standing waters. Various machine learning methods, including Generalised Linear Models, Support Vector Machines, Deep Learning, Decision Trees, Random Forest, and Gradient Boosted Trees, were tested. The Random Forest model performed best, with a correlation of 0.744 ± 0.11. Indicators related to landscape structure, such as diversity_mean (0.376) and relation_mean (0.292), had the highest global correlation weights, while LUI and land use change indicators like NirV2_mean (0.369) and NirV_regme (0.284) were also significant. All indicators and their effects on water quality (Chla) are discussed in detail. The study highlights the potential of the ESIS/Imalys tool for quantifying landscape structure, LUI, and land use change with RS to model and predict water quality and suggests directions for future model improvements by incorporating additional influencing factors.}, }
@article {pmid39777935, year = {2025}, author = {Mond, L and Geyer, S and Tetzlaff, J and Weißenborn, K and Schneider, J and Epping, J}, title = {More Drugs and Fewer Strokes? Time Trends in CVD Medication and Incidence of Stroke With German Health Insurance Data.}, journal = {Pharmacoepidemiology and drug safety}, volume = {34}, number = {1}, pages = {e70077}, doi = {10.1002/pds.70077}, pmid = {39777935}, issn = {1099-1557}, support = {//Allgemeine Ortskrankenkasse Niedersachsen/ ; GE 1167/15-1//Deutsche Forschungsgemeinschaft/ ; GE 1167/19-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; *Stroke/epidemiology/prevention & control ; Adult ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/prevention & control ; Young Adult ; Adolescent ; *Insurance, Health/statistics & numerical data ; Prevalence ; Cardiovascular Agents/therapeutic use/adverse effects ; Age Factors ; Time Factors ; Databases, Factual ; }, abstract = {BACKGROUND: Successful prevention of cardiovascular diseases (CVD) may reduce the burden of diseases. Preventive medication is an important measure to decrease the risks of cardiovascular events, in particular myocardial infarction and stroke. The aim of this study is to analyze the prevalence of CVD preventive medication in Germany over time with respect to sex and age and to compare it with the temporal development of strokes.
METHODS: The study is based on statutory health insurance claims data from the AOK Niedersachsen (AOKN) covering the years 2005-2018. The study population comprises all AOKN insured persons aged 18 years and older (N = 2 088 495). Age-standardized time trends of the prevalence of CVD preventive medication and incidence of stroke were calculated for men and women in different age groups. After that, the relationship of both measures was examined in an ecological correlation.
RESULTS: We found a clear increase in medication prevalence over time. In 2018, about 35% of the total population and about 85% of those over 85 years of age received CVD preventive medication. At the same time, age-standardized incidence rates of ischemic stroke were decreasing slightly. The ecological correlation showed a negative association between medication prevalence and stroke incidence especially in the higher age groups.
CONCLUSION: High correlation coefficients indicate that higher medication prevalence could be linked to better population health. Further research is needed to draw conclusions about the effects of increasing medicalization, including adverse risks and side effects at the population level.}, }
@article {pmid39776539, year = {2024}, author = {Chandel, N and Maile, A and Shrivastava, S and Verma, AK and Thakur, V}, title = {Establishment and perturbation of human gut microbiome: common trends and variations between Indian and global populations.}, journal = {Gut microbiome (Cambridge, England)}, volume = {5}, number = {}, pages = {e8}, doi = {10.1017/gmb.2024.6}, pmid = {39776539}, issn = {2632-2897}, abstract = {Human gut microbial species are crucial for dietary metabolism and biosynthesis of micronutrients. Digested products are utilised by the host as well as several gut bacterial species. These species are influenced by various factors such as diet, age, geographical location, and ethnicity. India is home to the largest human population in the world. It is spread across diverse ecological and geographical locations. With variable dietary habits and lifestyles, Indians have unique gut microbial composition. This review captures contrasting and common trends of gut bacterial community establishment in infants (born through different modes of delivery), and how that bacterial community manifests itself along infancy, through old age between Indian and global populations. Because dysbiosis of the gut community structure is associated with various diseases, this review also highlights the common and unique bacterial species associated with various communicable as well as noncommunicable diseases such as diarrhoea, amoebiasis, malnutrition, type 2 diabetes, obesity, colorectal cancer, inflammatory bowel disease, and gut inflammation and damage to the brain in the global and Indian population.}, }
@article {pmid39776261, year = {2025}, author = {Nolasco, M and Balzarini, M}, title = {Assessment of temporal aggregation of Sentinel-2 images on seasonal land cover mapping and its impact on landscape metrics.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {2}, pages = {142}, pmid = {39776261}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Ecosystem ; *Seasons ; Satellite Imagery ; Geographic Information Systems ; }, abstract = {Landscape metrics (LM) play a crucial role in fields such as urban planning, ecology, and environmental research, providing insights into the ecological and functional dynamics of ecosystems. However, in dynamic systems, generating thematic maps for LM analysis poses challenges due to the substantial data volume required and issues such as cloud cover interruptions. The aim of this study was to compare the accuracy of land cover maps produced by three temporal aggregation methods: median reflectance, maximum normalised difference vegetation index (NDVI), and a two-date image stack using Sentinel-2 (S2) and then to analyse their implications for LM calculation. The Google Earth Engine platform facilitated data filtering, image selection, and aggregation. A random forest algorithm was employed to classify five land cover classes across ten sites, with classification accuracy assessed using global measurements and the Kappa index. LM were then quantified. The analysis revealed that S2 data provided a high-quality, cloud-free dataset suitable for analysis, ensuring a minimum of 25 cloud-free pixels over the study period. The two-date and median methods exhibited superior land cover classification accuracy compared to the max NDVI method. In particular, the two-date method resulted in lower fragmentation-heterogeneity and complexity metrics in the resulting maps compared to the median and max NDVI methods. Nevertheless, the median method holds promise for integration into operational land cover mapping programmes, particularly for larger study areas exceeding the width of S2 swath coverage. We find patch density combined with conditional entropy to be particularly useful metrics for assessing fragmentation and configuration complexity.}, }
@article {pmid39771200, year = {2024}, author = {Sedmáková, D and Jaloviar, P and Mišíková, O and Šumichrast, L and Slováčková, B and Kucbel, S and Vencurik, J and Bosela, M and Sedmák, R}, title = {Small Gap Dynamics in High Mountain Central European Spruce Forests-The Role of Standing Dead Trees in Gap Formation.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {24}, pages = {}, doi = {10.3390/plants13243502}, pmid = {39771200}, issn = {2223-7747}, support = {APVV-21-0199//Slovak Research and Development Agency/ ; APVV-19-0183//Slovak Research and Development Agency/ ; APVV-20-0408//Slovak Research and Development Agency/ ; 1/0515/23//The Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, abstract = {Gap dynamics are driving many important processes in the development of temperate forest ecosystems. What remains largely unknown is how often the regeneration processes initialized by endogenous mortality of dominant and co-dominant canopy trees take place. We conducted a study in the high mountain forests of the Central Western Carpathians, naturally dominated by the Norway spruce. Based on the repeated forest inventories in two localities, we quantified the structure and amount of deadwood, as well as the associated mortality of standing dead canopy trees. We determined the basic specific gravity of wood and anatomical changes in the initial phase of wood decomposition. The approach for estimating the rate of gap formation and the number of canopy trees per unit area needed for intentional gap formation was formulated based on residence time analysis of three localities. The initial phase of gap formation (standing dead tree in the first decay class) had a narrow range of residence values, with a 90-95% probability that gap age was less than 10 or 13 years. Correspondingly, a relatively constant absolute number of 12 and 13 canopy spruce trees per hectare died standing in 10 years, with a mean diameter reaching 50-58 cm. Maximum diameters trees (70-80 cm) were represented by 1-4 stems per hectare. The values of the wood-specific gravity of standing trees were around 0.370-0.380 g.cm[-3], and varied from 0.302 to 0.523 g.cm[-3]. Microscopically, our results point out that gap formation is a continuous long-lasting process, starting while canopy trees are living. We observed early signs of wood degradation and bacteria, possibly associated with bark beetles, that induce a strong effect when attacking living trees with vigorous defenses. New information about the initial phase of gap formation has provided a basis for the objective proposal of intervals and intensities of interventions, designed to promote a diversified structure and the long-term ecological stability of the mountain spruce stands in changing climate conditions.}, }
@article {pmid39656924, year = {2025}, author = {Bastian, FB and Cammarata, AB and Carsanaro, S and Detering, H and Huang, WT and Joye, S and Niknejad, A and Nyamari, M and Mendes de Farias, T and Moretti, S and Tzivanopoulou, M and Wollbrett, J and Robinson-Rechavi, M}, title = {Bgee in 2024: focus on curated single-cell RNA-seq datasets, and query tools.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D878-D885}, pmid = {39656924}, issn = {1362-4962}, support = {//University of Lausanne/ ; U01CA215010/GF/NIH HHS/United States ; //Service de la Santé Publique, Canton de Vaud/ ; U01 CA215010/CA/NCI NIH HHS/United States ; 31003A_173048/SNSF_/Swiss National Science Foundation/Switzerland ; 863410//Horizon 2020 - Research and Innovation Framework Programme/ ; //swissuniversities Programme Open Science/ ; //SIB Swiss Institute of Bioinformatics/ ; }, mesh = {Animals ; *Single-Cell Analysis/methods ; *RNA-Seq/methods ; *Software ; *Databases, Genetic ; Humans ; Internet ; Molecular Sequence Annotation ; Gene Expression Profiling/methods ; Data Curation ; Single-Cell Gene Expression Analysis ; }, abstract = {Bgee (https://www.bgee.org/) is a database to retrieve and compare gene expression patterns in multiple animal species. Expression data are integrated and made comparable between species thanks to consistent data annotation and processing. In the past years, we have integrated single-cell RNA-sequencing expression data into Bgee through careful curation of public datasets in multiple species. We have fully integrated this new technology along with the wealth of other data existing in Bgee. As a result, Bgee can now provide one definitive answer all the way to the cell resolution about a gene's expression pattern, comparable between species. We have updated our programmatic access tools to adapt to these changes accordingly. We have introduced a new web interface, providing detailed access to our annotations and expression data. It enables users to retrieve data, e.g. for specific organs, cell types or developmental stages, and leverages ontology reasoning to build powerful queries. Finally, we have expanded our species count from 29 to 52, emphasizing fish species critical for vertebrate genome studies, species of agronomic and veterinary importance and nonhuman primates.}, }
@article {pmid39475188, year = {2025}, author = {Kemmler, E and Lemfack, MC and Goede, A and Gallo, K and Toguem, SMT and Ahmed, W and Millberg, I and Preissner, S and Piechulla, B and Preissner, R}, title = {mVOC 4.0: a database of microbial volatiles.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D1692-D1696}, pmid = {39475188}, issn = {1362-4962}, support = {Pi153/36-1//German Research Foundation/ ; //University of Rostock/ ; 428445448//Food allergy and tolerance (FOOD@)/ ; }, mesh = {*Volatile Organic Compounds/metabolism/chemistry ; *Bacteria/metabolism/genetics ; Microbiota ; Metabolomics/methods ; Databases, Factual ; Humans ; Metabolome ; Terpenes/metabolism/chemistry ; Databases, Chemical ; }, abstract = {Metabolomic microbiome research has become an important topic for understanding agricultural, ecological as well as health correlations. Only the determination of both the non-volatile and the volatile organic compound (mVOC) production by microorganisms allows a holistic view for understanding the complete potential of metabolomes and metabolic capabilities of bacteria. In the recent past, more and more bacterial headspaces and culture media were analyzed, leading to an accumulation of about 3500 mVOCs in the updated mVOC 4.0 database, including compounds synthesized by the newly discovered non-canonical terpene pathway. Approximately 10% of all mVOCs can be assigned with a biological function, some mVOCs have the potential to impact agriculture in the future (e.g. eco-friendly pesticides) or animal and human health care. mVOC 4.0 offers various options for exploring extensively annotated mVOC data from different perspectives, including improved mass spectrometry matching. The mVOC 4.0 database includes literature searches with additional relevant keywords, making it the most up-to-date and comprehensive publicly available mVOC platform at: http://bioinformatics.charite.de/mvoc.}, }
@article {pmid39470715, year = {2025}, author = {Miao, Z and Ren, Y and Tarabini, A and Yang, L and Li, H and Ye, C and Liti, G and Fischer, G and Li, J and Yue, JX}, title = {ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D852-D863}, pmid = {39470715}, issn = {1362-4962}, support = {32070592//National Natural Science Foundation of China/ ; 2022A1515010717//Guangdong Basic and Applied Basic Research Foundation/ ; 2019QN01Y183//Guangdong Pearl River Talents Program/ ; YTP-SYSUCC-0042//Sun Yat-sen University Cancer Center/ ; 24qnpy293//Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Saccharomyces cerevisiae/genetics/metabolism ; *Genome, Fungal ; *Databases, Genetic ; *Genomics/methods ; Telomere/genetics ; Molecular Sequence Annotation ; Proteomics ; Multiomics ; }, abstract = {As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.}, }
@article {pmid39761773, year = {2025}, author = {Banakar, SN and Karan, R and Prasanna Kumar, MK and Venkateshbabu, G and Harish, J and Patil, SS and Chandrashekar, BS and Mahesh, HB and Devanna, P and Manjunatha, C and Vamsidharreddy, N and Pallavi, KN and Sarangi, AN and Vaidya, K and Guru Murthy, DS}, title = {Unveiling Fusarium falciforme: Genome sequencing of a Novel wilt causing pathogen in Subabul (Leucaena leucocephala L.) in India.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107281}, doi = {10.1016/j.micpath.2025.107281}, pmid = {39761773}, issn = {1096-1208}, abstract = {Subabul (Leucaena leucocephala L.) is a leguminous species often referred to as the "miracle tree," it provides numerous ecosystem services and exhibits robust ecological characteristics. However, the infection caused by phytopathogenic fungi is poorly understood in Subabul. Therefore, this study provides comprehensive insights into the molecular and genomic characteristics of Fusarium falciforme, the causal agent of wilt disease in Subabul (Leucaena leucocephala). Pathogen isolation from infected samples, followed by morpho-molecular characterization through DNA sequencing of key markers (ITS, LSU, TEF1α) and phylogenetic analysis, confirmed the identity of F. falciforme. Host range analysis demonstrated the pathogen's ability to infect additional leguminous crops, including chickpea (Cicer arietinum) and soybean (Glycine max). A complete genome assembly revealed a genome size of 59.19 Mb, comprising 18,853 protein-coding genes. Comparative genomic analysis elucidated evolutionary relationships with other Fusarium species, while functional annotation identified critical virulence factors, such as polyketide synthases, ABC transporters, and secretory proteins, which facilitate host tissue invasion. These findings enhance the understanding of F. falciforme pathogenicity, enabling improved diagnostic tools and management strategies for controlling wilt disease in Subabul and related legumes.}, }
@article {pmid39761073, year = {2025}, author = {Sangeetha, S and Sajeev, S and Hamza, MK and Shome, BR and Raisen, C and Holmes, MA and Sivaraman, GK}, title = {Whole-Genome Sequencing of Antimicrobial Resistant Klebsiella quasipneumoniae, a Novel Sequence Type 5655 from Retail Fish Market, Assam, India.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2023.0017}, pmid = {39761073}, issn = {1556-7125}, abstract = {Klebsiella quasipneumoniae is a recently described species that can be differentiated from Klebsiella pneumoniae. However, in clinical settings, they are frequently misidentified as K. pneumoniae. In this study, our objective was to conduct genomic characterization and bioinformatics analysis of K. quasipneumoniae subsp. quasipneumoniae (KpII-A) isolated from a sample obtained from a retail fish market in Assam, India. Notably, this particular isolate was identified as K. pneumoniae when identified using BD Pheonix™ M50 (BD Difco, USA). This represents a serious pitfall of conventional microbiological methods for distinguishing between K. pneumoniae and K. quasipneumoniae. In this connection, identifying differences in nuclear gene content is key to avoid misidentification. The isolate was confirmed to be KpII-A using species identification by Mash Screen and whole-genome sequencing by the Illumina platform. We report the draft genome sequence of this strain, comprising of 53 contigs with an average GC content of 58.11%. The annotation revealed 5,095 protein coding sequences, 69 tRNA genes, and 4 rRNA genes. The isolated strain acknowledges the presence of oqxA, oqxB, fosA, and blaOKP-A-3 antimicrobial resistance genes (ARGs). Additionally two phage genomes were detected in contigs 3 and 19 of the bacterial genome. Based on the multilocus sequence typing and genome sequencing, the isolate was identified as a novel sequence type, ST5655, within the species K. quasipneumoniae under the phylogroup KpII-A. The presence of antimicrobial resistance genes in KpII-A, isolated from retail fish samples, raises concerns regarding transmission across barriers in ecological niches and possible transmission to consumers. Given that fish may serve as a potential vehicle for ARG transmission, our findings are highly relevant and paramount to human health. Moreover, our study supports the robustness of the sequence-based microbial identification.}, }
@article {pmid39753746, year = {2025}, author = {Allegretti, E and D'Innocenzo, G and Coco, MI}, title = {The Visual Integration of Semantic and Spatial Information of Objects in Naturalistic Scenes (VISIONS) database: attentional, conceptual, and perceptual norms.}, journal = {Behavior research methods}, volume = {57}, number = {1}, pages = {42}, pmid = {39753746}, issn = {1554-3528}, support = {PTDC/PSI-ESP/30958/2017//Fundação para a Ciência e a Tecnologia/ ; LISBOA-01-0145-FEDER-0309//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Humans ; *Semantics ; *Attention/physiology ; Female ; Adult ; Male ; Young Adult ; *Space Perception/physiology ; *Visual Perception/physiology ; Databases, Factual ; Eye-Tracking Technology ; Adolescent ; }, abstract = {The complex interplay between low- and high-level mechanisms governing our visual system can only be fully understood within ecologically valid naturalistic contexts. For this reason, in recent years, substantial efforts have been devoted to equipping the scientific community with datasets of realistic images normed on semantic or spatial features. Here, we introduce VISIONS, an extensive database of 1136 naturalistic scenes normed on a wide range of perceptual and conceptual norms by 185 English speakers across three levels of granularity: isolated object, whole scene, and object-in-scene. Each naturalistic scene contains a critical object systematically manipulated and normed regarding its semantic consistency (e.g., a toothbrush vs. a flashlight in a bathroom) and spatial position (i.e., left, right). Normative data are also available for low- (i.e., clarity, visual complexity) and high-level (i.e., name agreement, confidence, familiarity, prototypicality, manipulability) features of the critical object and its embedding scene context. Eye-tracking data during a free-viewing task further confirms the experimental validity of our manipulations while theoretically demonstrating that object semantics is acquired in extra-foveal vision and used to guide early overt attention. To our knowledge, VISIONS is the first database exhaustively covering norms about integrating objects in scenes and providing several perceptual and conceptual norms of the two as independently taken. We expect VISIONS to become an invaluable image dataset to examine and answer timely questions above and beyond vision science, where a diversity of perceptual, attentive, mnemonic, or linguistic processes could be explored as they develop, age, or become neuropathological.}, }
@article {pmid38979368, year = {2024}, author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M}, title = {Eco-evolutionary Guided Pathomics Analysis to Predict DCIS Upstaging.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38979368}, issn = {2692-8205}, support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; }, abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. In this study, we show that ecological habitat analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, we identified cancer cells with metabolic phenotypes attributed to their habitat conditions, such as the expression of CA9 indicating hypoxia responding phenotype, and LAMP2b indicating the acid adaptation. Traditionally these markers have shown limited predictive capabilities for DCIS upstaging, if any. However, when analyzed from an ecological perspective, their power to differentiate between pure DCIS and upstaged DCIS increased significantly. Second, using eco-evolutionary guided computational and digital pathology techniques, we discovered distinct niches with spatial patterns of these biomarkers and used the distribution of such niches to predict patient upstaging. The niches patterns were characterized by pattern analysis of both cellular and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve (AUC) of 0.74. Our results affirm the importance of using eco-evolutionary-designed approaches in biomarkers discovery studies in the era of digital pathology by demonstrating the role of tumor ecological habitats and niches.}, }
@article {pmid39753915, year = {2025}, author = {Davidson, SC and Cagnacci, F and Newman, P and Dettki, H and Urbano, F and Desmet, P and Bajona, L and Bryant, E and Carneiro, APB and Dias, MP and Fujioka, E and Gambin, D and Hoenner, X and Hunter, C and Kato, A and Kot, CY and Kranstauber, B and Lam, CH and Lepage, D and Naik, H and Pye, JD and Sequeira, AMM and Tsontos, VM and van Loon, E and Vo, D and Rutz, C}, title = {Establishing bio-logging data collections as dynamic archives of animal life on Earth.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {39753915}, issn = {2397-334X}, support = {80NSSC21K1182//National Aeronautics and Space Administration (NASA)/ ; Fellowship at Fondation IméRA//Institut de Recherche pour le Développement (French Research Institute for Development)/ ; CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)/ ; LifeWatch//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; DP210103091//Department of Education and Training | Australian Research Council (ARC)/ ; GBMF9881//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; NGS-82515R-20//National Geographic Society/ ; }, abstract = {Rapid growth in bio-logging-the use of animal-borne electronic tags to document the movements, behaviour, physiology and environments of wildlife-offers opportunities to mitigate biodiversity threats and expand digital natural history archives. Here we present a vision to achieve such benefits by accounting for the heterogeneity inherent to bio-logging data and the concerns of those who collect and use them. First, we can enable data integration through standard vocabularies, transfer protocols and aggregation protocols, and drive their wide adoption. Second, we need to develop integrated data collections on standardized data platforms that support data preservation through public archiving and strategies that ensure long-term access. We outline pathways to reach these goals, highlighting the need for resources to govern community data standards and guide data mobilization efforts. We propose the launch of a community-led coordinating body and provide recommendations for how stakeholders-including government data centres, museums and those who fund, permit and publish bio-logging work-can support these efforts.}, }
@article {pmid39753264, year = {2025}, author = {Aguirre Vergara, F and Pinker, I and Fischer, A and Seuring, T and Tichomirowa, MA and de Beaufort, C and Kamp, SM and Fagherazzi, G and Aguayo, GA}, title = {Readiness of adults with type 1 diabetes and diabetes caregivers for diabetes distress monitoring using a voice-based digital health solution: insights from the PsyVoice mixed methods study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e088424}, doi = {10.1136/bmjopen-2024-088424}, pmid = {39753264}, issn = {2044-6055}, abstract = {OBJECTIVES: Diabetes distress can negatively affect the well-being of individuals with type 1 diabetes (T1D). Voice-based (VB) technology can be used to develop inexpensive and ecological tools for managing diabetes distress. This study explored the competencies to engage with digital health services, needs and preferences of individuals with T1D or caring for a child with this condition regarding VB technology to inform the tailoring of a co-designed tool for supporting diabetes distress management.
DESIGN: We used a mixed methods design. We performed a qualitative reflexive thematic analysis of semistructured interviews of people living with T1D or caring for a child with T1D, complemented by quantitative analysis (descriptive statistics).
SETTING: 12 adults living with T1D who attended diabetes centres or cared for a child with this condition participated in semistructured interviews to collect opinions about voice technology. They also responded to three questionnaires on sociodemographics and diabetes management, diabetes distress and e-health literacy.
OUTCOME MEASURES: Main: Patient experiences and perceptions derived from the coded transcriptions of interview data. Secondary: Quantitative data generated from Socio-Demographic and Diabetes Management questionnaire; Problem Areas in Diabetes Scale and e-Health Literacy Questionnaire.
RESULTS: Five major themes were generated from the participants' interview responses: (1) Experience of T1D, (2) Barriers to VB technology use, (3) Facilitators of VB technology, (4) Expectations of VB technology management in T1D, (5) Role of healthcare professionals in implementing VB technology for T1D. Most participants expressed a favourable view of voice technology for diabetes distress management. Trust in technology and healthcare professionals emerged as the predominant sentiment, with participants' current device type impacting anticipated barriers to adopting new technologies.
CONCLUSION: The results highlighted positive participant views towards VB technology. Device use, previous experience and health professional endorsement were influential facilitators of novel VB digital health solutions. Further research involving younger people with T1D could further contribute to the successful development of these tools.
TRIAL REGISTRATION NUMBER: ClinicalTrials.gov, NCT05517772.}, }
@article {pmid39749768, year = {2025}, author = {Fifield, K and Veerakanjana, K and Hodsoll, J and Kuntsi, J and Tye, C and Simblett, S}, title = {Completion Rates of Smart Technology Ecological Momentary Assessment (EMA) in Populations With a Higher Likelihood of Cognitive Impairment: A Systematic Review and Meta-Analysis.}, journal = {Assessment}, volume = {}, number = {}, pages = {10731911241306364}, doi = {10.1177/10731911241306364}, pmid = {39749768}, issn = {1552-3489}, abstract = {Ecological Momentary Assessment using smartphone technology (smart EMA) has grown substantially over the last decade. However, little is known about the factors associated with completion rates in populations who have a higher likelihood of cognitive impairment. A systematic review of Smart EMA studies in populations who have a higher likelihood of cognitive impairment was carried out (PROSPERO; ref no CRD42022375829). Smartphone EMA studies in neurological, neurodevelopmental and neurogenetic conditions were included. Six databases were searched, and bias was assessed using Egger's test. Completion rates and moderators were analyzed using meta-regression. Fifty-five cohorts were included with 18 cohorts reporting confirmed cognitive impairment. In the overall cohort, the completion rate was 74.4% and EMA protocol characteristics moderated completion rates. Participants with cognitive impairment had significantly lower completion rates compared with those without (p = .021). There were no significant moderators in the cognitive impairment group. Limitations included significant methodological issues in reporting of completion rates, sample characteristics, and associations with completion and dropout rates. These findings conclude that smart EMA is feasible for people with cognitive impairment. Future research should focus on the efficacy of using smart EMA within populations with cognitive impairment to develop an appropriate methodological evidence base.}, }
@article {pmid39747897, year = {2025}, author = {Petrovic, M and Salovic, B and Tomic, A and Jesic-Petrovic, T and Matejic, A and Radovic, I and Babic, S and Korugic, A and Jelovac, D and Mikovic, N and Jakovljevic, S and Pelemis, S and Dimitrijevic, M and Milovanovic, J and Jotic, A and Trivic, A and Dimitrijevic, A and Bulatovic, S and Dudvarski, Z and Soldatovic, I and Ilic-Zivojinovic, J}, title = {Functional assessment of cancer therapy - head & neck (FACT-HN) translation and validation in Serbian.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {298}, pmid = {39747897}, issn = {2045-2322}, mesh = {Humans ; *Head and Neck Neoplasms/therapy/psychology ; Male ; Serbia ; Female ; *Quality of Life ; Middle Aged ; *Psychometrics/methods ; Surveys and Questionnaires ; Aged ; Reproducibility of Results ; Adult ; Translations ; }, abstract = {This study aimed to translate and validate the Functional Assessment of Cancer Therapy - Head & Neck (FACT-HN) in a Serbian-speaking population, assessing its psychometric properties and utility in evaluating the quality of life in head and neck cancer patients. The research focuses on determining the translated questionnaire's reliability, validity, and cultural relevance. A total of 106 Serbian-speaking head and neck cancer patients completed the translated FACT-HN, along with other validated instruments, including the EORTC QLQ-C30, EORTC QLQ-HN43, CES-D, and GAD-7. The translation followed a standard internationally accepted procedure. Psychometric analyses were conducted using confirmatory and exploratory factor analysis, Pearson correlations, and reliability measures such as Cronbach's alpha and intraclass correlation coefficients. The Serbian version of the FACT-HN showed excellent internal consistency across all subscales, with Cronbach's alpha ranging from 0.70 to 0.89. Confirmatory factor analysis confirmed the five-factor structure. Strong correlations were observed between the FACT-HN and other validated QoL measures, particularly with the EORTC QLQ-C30 and EORTC QLQ-HN43. Convergent validity was satisfactory for all components except the Social Well-Being component. The Serbian version of the FACT-HN is a valid and reliable tool for assessing the quality of life in head and neck cancer patients. It provides a comprehensive assessment of physical, social, emotional, and functional well-being, making it valuable for clinical and research applications in Serbian-speaking populations. Further research is needed to assess its sensitivity to longitudinal treatment-related changes.}, }
@article {pmid39747514, year = {2025}, author = {Liu, X and Tan, Y and Dong, J and Wu, J and Wang, X and Sun, Z}, title = {Assessing habitat selection parameters of Arabica coffee using BWM and BCM methods based on GIS.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8}, pmid = {39747514}, issn = {2045-2322}, support = {51979133//National Natural Science Foundation of China/ ; 202301AS070030//Yunnan Fundamental Research Projects/ ; 202302AE090024//Yunnan Major Science and Technology Special Plan/ ; }, mesh = {*Ecosystem ; *Geographic Information Systems ; *Coffea/growth & development ; China ; Coffee ; Climate ; Decision Making ; Conservation of Natural Resources/methods ; Soil/chemistry ; }, abstract = {Arabica coffee, as one of the world's three native coffee species, requires rational planning for its growing areas to ensure ecological and sustainable agricultural development. This study aims to establish a decision-making framework using Geographic Information Systems (GIS) and Multi-Criteria Decision-Making (MCDM), with a focus on assessing the habitat suitability of Arabica coffee in Yunnan Province, China. The impacts of climate, topography, soil, and socio-economic factors were considered by selecting 13 criteria through correlation analysis. Indicator weights were determined using the Best-Worst Method (BWM), while weighted processing was conducted using the Base-Criterion Method (BCM). Sensitivity analysis was performed to verify the accuracy and stability of the model. Additionally, several decision models were evaluated to investigate regionalizing Arabica coffee habitats in Yunnan. The results highlighted that minimum temperature during the coldest month is crucial for evaluation purposes. The BWM-GIS model identified suitable areas comprising 13.55% of the total area as most suitable, 27.46% as suitable, and 59.00% as unsuitable, whereas corresponding values for the BCM-GIS model were 9.97%, 30.43%, and 59.59%. Despite employing different decision-making methods, both models yielded similar and consistent results. The suitable areas mainly encompass Dehong, Pu'er, Lincang, Xishuangbanna, Baoshan, southern Chuxiong, eastern Honghe, southern Yuxi, and parts of Wenshan. BWM-GIS achieved an area under curve (AUC) value of 0.891, while BCM-GIS obtained an AUC value of 0.890, indicating the stability and reliability of the models. Among them, the evaluation process of BCM-GIS was simpler and more realistic. Therefore, it has high feasibility and practical value in practical application. The findings from this study provide a significant scientific foundation for optimizing Yunnan Province.}, }
@article {pmid39373541, year = {2025}, author = {Zuo, YW and Quan, MH and Liu, GH and Zhang, X and Long, NN and You, SQ and Peng, Y and Deng, HP}, title = {Multi-Omics Analysis Reveals Molecular Responses of Alkaloid Content Variations in Lycoris aurea Across Different Locations.}, journal = {Plant, cell & environment}, volume = {48}, number = {2}, pages = {953-964}, doi = {10.1111/pce.15187}, pmid = {39373541}, issn = {1365-3040}, support = {//This study was supported by General Program of the Chongqing Natural Science Foundation and National Natural Science Foundation of China./ ; }, mesh = {*Lycoris/metabolism/genetics ; *Alkaloids/metabolism ; Gene Expression Regulation, Plant ; Metabolomics ; Transcriptome ; Soil Microbiology ; Protein Interaction Maps ; Gene Expression Profiling ; Photosynthesis ; Metabolome ; Genes, Plant ; Multiomics ; }, abstract = {Lycoris aurea, celebrated for its visually striking flowers and significant medicinal value due to the presence of alkaloids such as lycorine and galanthamine, has intricate yet poorly understood regulatory mechanisms. This study provides a detailed examination of the transcriptomic, metabolomic and ecological dynamics of L. aurea, aiming to elucidate the underlying molecular mechanisms of alkaloid biosynthesis. Our comparative analysis across different ecological settings highlighted key genes involved in alkaloid biosynthesis, such as genes encoding aldehyde dehydrogenase and norbelladine 4'-O-methyltransferase, which were distinctively increased in the high alkaloids-producing group. We identified a total of 6871 differentially expressed genes and 915 metabolites involved in pathways like terpenoid backbone biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. Protein interaction network analysis revealed significant upregulation of photosynthesis, photosystem and photosynthetic membrane pathways in the alkaloids-producing region. Furthermore, our research delineated the interactions among soil microbial communities, genes and plant and soil biochemical properties, noting that bacterial populations correlate with soil properties that favour the activation of metabolic pathways essential for alkaloid production. Collectively, this study advances our understanding of the genetic and metabolic alkaloid biosynthesis pathways in L. aurea, shedding light on the complex interactions that govern alkaloid production.}, }
@article {pmid39746011, year = {2025}, author = {Wohltjen, S and Colón, YI and Zhu, Z and Miller, K and Huang, WC and Mutlu, B and Li, Y and Niedenthal, PM}, title = {Uniting theory and data: the promise and challenge of creating an honest model of facial expression.}, journal = {Cognition & emotion}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/02699931.2024.2446945}, pmid = {39746011}, issn = {1464-0600}, abstract = {People routinely use facial expressions to communicate successfully and to regulate other's behaviour, yet modelling the form and meaning of these facial behaviours has proven surprisingly complex. One reason for this difficulty may lie in an over-reliance on the assumptions inherent in existing theories of facial expression - specifically that (1) there is a putative set of facial expressions that signal an internal state of emotion, (2) patterns of facial movement have been empirically linked to the prototypical emotions in this set, and (3) static, non-social, posed images from convenience samples are adequate to validate the first two assumptions. These assumptions have guided the creation of datasets, which are then used to train unrepresentative computational models of facial expression. In this article, we discuss existing theories of facial expression and review how they have shaped current facial expression recognition tools. We then discuss the resources that are available to help researchers build a more ecologically valid model of facial expressions.}, }
@article {pmid39736019, year = {2024}, author = {Kobzeva, K and Ivenkov, M and Gromov, R and Bushueva, O}, title = {HSP90 Family Members, Their Regulators and Ischemic Stroke Risk: A Comprehensive Molecular-Genetics and Bioinformatics Analysis.}, journal = {Frontiers in bioscience (Scholar edition)}, volume = {16}, number = {4}, pages = {19}, doi = {10.31083/j.fbs1604019}, pmid = {39736019}, issn = {1945-0524}, support = {22-15-00288//Russian Science Foundation/ ; }, mesh = {Humans ; *Polymorphism, Single Nucleotide ; *HSP90 Heat-Shock Proteins/genetics/metabolism ; *Ischemic Stroke/genetics ; Male ; Female ; Middle Aged ; *Computational Biology ; Aged ; *Genetic Predisposition to Disease ; Russia/epidemiology ; Risk Factors ; Case-Control Studies ; Heat Shock Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Disruptions in proteostasis are recognized as key drivers in cerebro- and cardiovascular disease progression. Heat shock proteins (HSPs), essential for maintaining protein stability and cellular homeostasis, are pivotal in neuroperotection. Consequently, deepening the understanding the role of HSPs in ischemic stroke (IS) risk is crucial for identifying novel therapeutic targets and advancing neuroprotective strategies.
AIM: Our objective was to examine the potential correlation between single nucleotide polymorphisms (SNPs) in genes that encode members of the Heat shock protein 90 (HSP90), small heat shock proteins (HSPB), and heat shock factors (HSF) families, and the risk and clinical characteristics of IS.
METHODS: 953 IS patients and 1265 controls from Central Russia were genotyped for nine SNPs in genes encoding HSP90AA1, HSFs, and HSPBs using the MassArray-4 system and probe-based polymerase chain reaction (PCR).
RESULTS: In smokers, SNP rs1133026 HSPB8 increased the risk of IS (risk allele A, odds ratio (OR) = 1.43, 95% Confidence Interval (CI) 1.02-2.02, p = 0.035), and rs556439 HSF2 increased the brain infarct size (risk allele A, p = 0.02). In non-smokers, SNPs rs4279640 HSF1 (protective allele T, OR = 0.58, 95% CI 0.37-0.92, p = 0.02) and rs4264324 HSP90AA1 (protective allele C, OR = 0.11, 95% CI 0.01-0.78, p = 0.001) lowered the risk of recurrent stroke; SNP rs7303637 HSPB8 increased the age of onset of IS (protective allele T, p = 0.04). In patients with body mass index (BMI) ≥25, SNPs rs556439 HSF2 (risk allele A, OR = 1.33, 95% CI 1.04-1.69, p = 0.02) and rs549302 HSF2 (risk allele G, OR = 1.34, 95% CI 1.02-1.75, p = 0.03) were linked to a higher risk of IS.
CONCLUSIONS: The primary molecular mechanisms through which the studied SNPs contribute to IS pathogenesis were found to be the regulation of cell death, inflammatory and oxidative stress responses.}, }
@article {pmid39730727, year = {2024}, author = {Kato, H}, title = {Daily walking time effects of the opening of a multifunctional facility "ONIKURU" using propensity score matching and GPS tracking techniques.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31047}, pmid = {39730727}, issn = {2045-2322}, support = {24K17421//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Female ; *Walking/physiology ; Male ; Adult ; *Geographic Information Systems ; *Propensity Score ; Middle Aged ; Young Adult ; Exercise/physiology ; Adolescent ; Environment Design ; Time Factors ; Smartphone ; }, abstract = {Urban design focused on improving walkability has received attention as a method of increasing physical activity among the population. However, only a few studies have examined the effect of walking time of opening multifunctional facilities as an architecture-scale intervention. This study aimed to clarify the effect of opening a multifunctional facility on residents' daily walking time. In addition, this study analyzed the gender and age subgroups. The natural experiment was conducted using the case of the Ibaraki City Cultural and Childcare Complex "ONIKURU," a public multifunctional facility. This study used GPS-trajectory data based on GPS tracking techniques, which is anonymized location data for smartphone users. The causal relationship was analyzed using propensity score matching and difference-in-differences analysis. The results showed that the opening of ONIKURU significantly increased the average walking time of visitors to 3.165 [- 1.697, 8.027] min/day compared with that of non-visitors. Specifically, visitors' average daily walking time improved to a level comparable to that of non-visitors after the opening of ONIKURU. In addition, opening ONIKURU significantly increased female young adults' average walking time to 3.385 [- 4.906, 11.676] min/day. Therefore, this study provides theoretical contributions to a health-promoting built environment significantly affecting walking at an architecture-scale intervention.}, }
@article {pmid39729740, year = {2024}, author = {Gupta, AK and Ravikumar, K and Gopal, V and Begum, N and Tabassum, and Sangeetha, S and Narendran, P and Shankar, D}, title = {A trans-disciplinary agro-ecology strategy to grow medicinal plants.}, journal = {Journal of Ayurveda and integrative medicine}, volume = {16}, number = {1}, pages = {100985}, doi = {10.1016/j.jaim.2024.100985}, pmid = {39729740}, issn = {0975-9476}, abstract = {The scope of the emerging field of Ayurvedic-biology visualized thus far is confined to studies on dimensions pertaining to clinical and experimental pharmacology, basic trans-disciplinary science and drug design. However, given the multiple facets of classical Ayurveda knowledge system, its application in the field of organic agriculture perhaps also needs to be urgently explored. The urgency is due to the growing public acceptance of Ayurveda as a preferred clinical choice for well-being and disease management. The turnover of the sector across manufacturing and health services is estimated to be around Rs.1,00,000 crores per annum. Medicinal plants today and in the coming decade will therefore be required in large volumes and given that their applications are solely for enhancing health of humans, livestock (Pashu Ayurveda) and crops (Vriksh Ayurveda), it is imperative that they be cultivated in an organic manner employing the fusion of best available inter-cultural knowledge. The Ayurvedic subjects relevant for organic agriculture are Desh vichar, Dravya guna Shastra and Vriksh Ayurveda. From the perspective of modern biology subjects like soil micro biome, genetics, plant physiology and the natural geographical distribution of species are relevant. It must be stated at the very outset that this article is largely theoretical. While experiments in Vriksh Ayurveda have been attempted on a small scale, the fusion of Ayurveda and biology for improving organic agriculture of medicinal plants has thus far not been systematically explored.}, }
@article {pmid39727132, year = {2024}, author = {Xin, PY and Tian, T and Zhang, ML and Han, WZ and Song, YT}, title = {[Assessment of habitat quality changes and driving factors in Jilin Province based on InVEST model and geodetector].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2853-2860}, doi = {10.13287/j.1001-9332.202410.026}, pmid = {39727132}, issn = {1001-9332}, mesh = {China ; *Ecosystem ; *Conservation of Natural Resources ; *Models, Theoretical ; Environmental Monitoring ; Forests ; Trees/growth & development ; Geographic Information Systems ; }, abstract = {Jilin Province is an important ecological security barrier in Northeast China as it is located at the junction of the Northeast forest belts and the northern sand prevention belts. In recent years, Jilin Province has actively carried out ecological protection and restoration projects, resulting in a continuous improvement trend for the overall ecological environment. However, the evolution patterns and mechanisms of habitat quality are largely unkown. We applied the InVEST model and geographic detector method to analyze the changes in habitat quality and evaluate the main driving factors from 2000 to 2020. The results showed that the average habitat quality in Jilin Province showed a slight downward trend, and that the spatial heterogeneity characteristics of habitat quality in east and west gradually increased. The degree of habitat degradation presented a single nuclear radiation pattern centered on Changchun City. Vegetation factors and terrain factors were the first and secondary causes of spatial heterogeneity of habitat quality, respectively. The average habitat quality within the eco-redline of Jilin Province was showing an increasing trend year by year, which was consistent with the overall distribution of regions with extremely high habitat quality levels. There was a local spatial dislocation (the phenomenon of extremely high habitat quality levels not within the eco-redline) in the eastern part of Jilin Province. Our results could provide reference basis for ecosystem protection and the spatial pattern optimization.}, }
@article {pmid39727130, year = {2024}, author = {Jia, J and Su, X and Zhang, J and Lu, CL and Zhang, MY and Li, X and Dong, YG and Ren, HC}, title = {[Land use changes and driving forces of landslide area in Tongwei County, Gansu Province, Northwest China from 1985 to 2020.].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {10}, pages = {2833-2841}, doi = {10.13287/j.1001-9332.202410.020}, pmid = {39727130}, issn = {1001-9332}, mesh = {China ; *Landslides ; *Conservation of Natural Resources ; *Crops, Agricultural/growth & development ; Ecosystem ; Trees/growth & development ; Forests ; Grassland ; Environmental Monitoring/methods ; Disasters ; Geographic Information Systems ; Poaceae/growth & development ; }, abstract = {Accurately analyzing the type of land use and change characteristics of disaster damage in landslide areas is of great significance to scientifically promote the optimization of regional land use pattern and disaster prevention and mitigation. We analyzed the characteristic parameters of landslides as well as the characteristics and driving factors of land use change from 1985 to 2020 in Tongwei County, Gansu Province, using ALOS DEM data and 1985-2020 land use data, GIS spatial analysis, land-use dynamic attitude, transfer matrix, and Geodetector. The results showed that a total of 1012 landslide samples were identified, characterized by medium elevation, gentle gradient, low elevation difference, short length, and small size. During 1985-2020, landslide area land use types were cropland, woodland, grassland, bare land and impervious surface, dominated by grassland and cropland. During 2015-2020, each category of single land use dynamic attitude reached the largest, with the value of cropland, grassland, woodland, bare land, and the combined land use being 3.1%, 3.0%, 10.9%, 20.0%, 1.5%, respectively. During the study period, land use change was dominated by cropland and grassland, with a total reduction of 4.39 km[2] in cultivated land area, which was converted into grassland and forest. There was no change in bare land and impervious surfaces. We investigated the driving factors of land use change across 2000-2005 and 2015-2020. Slope and normalized difference vegetation index had a stronger explanatory power for land use change during 2000-2005, while slope, population density and total population had a stronger explanatory power during 2015-2020. The land use mode of regional individual landslide tended to be unified, and the increase of grassland enhanced the vegetation cover of the region. The findings would provide a scientific basis for the development and reuse of disaster damaged land and ecological restoration.}, }
@article {pmid39720717, year = {2024}, author = {Luo, Z and Zhou, F and Jiang, S and Huang, J and Yang, L and Yang, Q and Shi, J and Li, E and Ma, Z and Li, Y}, title = {Immune and physiological responses in Penaeus monodon to ammonia-N stress: a multi-omics approach.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1510887}, pmid = {39720717}, issn = {1664-3224}, mesh = {Animals ; *Penaeidae/immunology ; *Ammonia/metabolism ; *Stress, Physiological/immunology ; *Oxidative Stress ; Transcriptome ; Metabolomics ; Immunity, Innate ; Gene Expression Profiling ; Nitrogen/metabolism ; Aquaculture ; Biomarkers ; Hepatopancreas/immunology/metabolism ; Multiomics ; }, abstract = {Ammonia-N stress is a significant environmental factor that adversely affects the health and productivity of aquaculture species. This study investigates the effects of ammonia-N stress on the shrimp Penaeus monodon through a combination of biochemical, histological, transcriptomic, and metabolomic analyses. Shrimp were exposed to ammonia-N stress for 12 and 96 hours, and key markers of oxidative stress, nitrogen metabolism, immune response, and overall health were assessed. The results showed that prolonged ammonia-N exposure causes significant hepatopancreatic damage, including atrophy and deformation. Transcriptomic analysis revealed significant changes in gene expression related to apoptosis, immune response, and key metabolic pathways, with particular emphasis on the disruption of innate immune signaling and defense mechanisms. Metabolomic analysis identified disruptions in nucleotide turnover, antioxidant defenses, and fundamental metabolic processes. These findings suggest that ammonia-N stress induces a multifaceted stress response in shrimp, involving oxidative stress, immune activation, and metabolic disturbances. Understanding these immune-related and metabolic mechanisms provides valuable insights into the molecular responses of crustaceans to environmental stress, laying the foundation for assessing the ecological risk of ammonia-N and identifying potential immunological biomarkers for monitoring and mitigating its adverse effects in aquaculture systems.}, }
@article {pmid39719706, year = {2024}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100725}, doi = {10.1016/j.xgen.2024.100725}, pmid = {39719706}, issn = {2666-979X}, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, }
@article {pmid39718830, year = {2024}, author = {Kicsiny, R and Hufnagel, L and Lóczi, L and Székely, L and Varga, Z}, title = {Modeling the Mutation and Competition of Certain Nutrient-Producing Protocells by Means of Specific Turing Machines.}, journal = {Artificial life}, volume = {}, number = {}, pages = {1-29}, doi = {10.1162/artl_a_00463}, pmid = {39718830}, issn = {1530-9185}, abstract = {It is very important to model the behavior of protocells as basic lifelike artificial organisms more and more accurately from the level of genomes to the level of populations. A better understanding of basic protocell communities may help us in describing more complex ecological systems accurately. In this article, we propose a new comprehensive, bilevel mathematical model of a community of three protocell species (one generalist and two specialists). The aim is to achieve a model that is as basic/fundamental as possible while already displaying mutation, selection, and complex population dynamics phenomena (like competitive exclusion and keystone species). At the microlevel of genetic codes, the protocells and their mutations are modeled with Turing machines (TMs). The specialists arise from the generalist by means of mutation. Then the species are put into a common habitat, where, at the macrolevel of populations, they have to compete for the available nutrients, a part of which they themselves can produce. Because of different kinds of mutations, the running times of the species as TMs (algorithms) are different. This feature is passed on to the macrolevel as different reproduction times. At the macrolevel, a discrete-time dynamic model describes the competition. The model displays complex lifelike behavior known from population ecology, including the so-called competitive exclusion principle and the effect of keystone species. In future works, the bilevel model will have a good chance of serving as a simple and useful tool for studying more lifelike phenomena (like evolution) in their pure/abstract form.}, }
@article {pmid39717656, year = {2024}, author = {Nguyen, TTT and de A Santiago, ALCM and Hallsworth, JE and Cordeiro, TRL and Voigt, K and Kirk, PM and Crous, PW and Júnior, MAM and Elsztein, C and Lee, HB}, title = {New Mucorales from opposite ends of the world.}, journal = {Studies in mycology}, volume = {109}, number = {}, pages = {273-321}, pmid = {39717656}, issn = {0166-0616}, abstract = {The Mucorales is a group of ancient fungi with global distribution. In the current study we accessed mucoralean fungi isolated from two countries on opposite sides of the Earth and in different hemispheres: South Korea and Brazil. Mucorales isolates were obtained from freshwater, soil, invertebrates, and fruit seeds and identified using phenotypic techniques combined with the DNA sequence data. These analyses revealed 15 new species including one that we affiliated to a newly proposed genus, Neofennellomyces. Names proposed for these 15 new species are Absidia cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, A. tarda, A. variiprojecta, A. variispora, Backusella varians, Mucor albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and Neofennellomyces jeongsukae. Of these new species, 12 were isolated from South Korea: A. cheongyangensis, A. fluvii, A. kunryangriensis, A. paracylindrospora, B. varians, M. albicolonia, M. aurantiacus, M. cryophilus, M. glutinatus, M. paraorantomantidis, M. timomeni, and N. jeongsukae, and three from Brazil: A. tarda, A. variiprojecta, and A. variispora. Niche specificity of these fungi is discussed including newly recorded invertebrate hosts and a new geographic distribution for species of Backusella, Circinella, Cunninghamella, and Mucor. Given these findings, we provide an inventory of Mucorales. Taxonomic novelties: New genus: Neofennellomyces Hyang B. Lee & T.T.T. Nguyen. New species: Absidia cheongyangensis Hyang B. Lee & T.T.T. Nguyen, Absidia fluvii Hyang B. Lee, A.L. Santiago, P.M. Kirk, K. Voigt & T.T.T. Nguyen, Absidia kunryangriensis Hyang B. Lee & T.T.T. Nguyen, Absidia paracylindrospora Hyang B. Lee & T.T.T. Nguyen, Absidia tarda T.R.L. Cordeiro, Hyang B. Lee & A.L. Santiago, Absidia variiprojecta T.R.L. Cordeiro & A.L. Santiago, Absidia variispora T.R.L. Cordeiro & A.L. Santiago, Backusella varians Hyang B. Lee & T.T.T. Nguyen, Mucor aurantiacus Hyang B. Lee & T.T.T. Nguyen, Mucor cryophilus Hyang B. Lee & T.T.T. Nguyen, Mucor albicolonia Hyang B. Lee & T.T.T. Nguyen, Mucor glutinatus Hyang B. Lee & T.T.T. Nguyen, Mucor paraorantomantidis Hyang B. Lee & T.T.T. Nguyen, Mucor timomeni Hyang B. Lee & T.T.T. Nguyen, Neofennellomyces jeongsukae Hyang B. Lee & T.T.T. Nguyen. Citation: Nguyen TTT, de A. Santiago ALCM, Hallsworth JE, Cordeiro TRL, Voigt K, Kirk PM, Crous PW, Júnior MAM, Elsztein C, Lee HB (2024). New Mucorales from opposite ends of the world. Studies in Mycology 109: 273-321. doi: 10.3114/sim.2024.109.04.}, }
@article {pmid39717508, year = {2025}, author = {Wang, T and Campbell, C and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Jaworski, J and Glampson, B and Papadimitriou, D and Mercuri, L and Mayer, E and Jones, CR and Salih, H and Roadknight, G and Little, S and Noble, T and Várnai, KA and Davis, C and Heinson, AI and George, M and Borca, F and English, L and Romão, L and Ramlakhan, D and , and Woods, K and Davies, J and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Barnes, E and Matthews, PC}, title = {Distinct virologic trajectories in chronic hepatitis B identify heterogeneity in response to nucleos(t)ide analogue therapy.}, journal = {JHEP reports : innovation in hepatology}, volume = {7}, number = {1}, pages = {101229}, pmid = {39717508}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: The dynamics of HBV viral load (VL) in patients with chronic hepatitis B (CHB) on nucleos(t)ide analogue (NA) treatment and its relationship with liver disease are poorly understood. We aimed to study longitudinal VL patterns and their associations with CHB clinical outcomes.
METHODS: Utilising large scale, routinely collected electronic health records from six centres in England, collated by the National Institute for Health and Care Research Health Informatics Collaborative (NIHR HIC), we applied latent class mixed models to investigate VL trajectory patterns in adults receiving NA treatment. We assessed associations of VL trajectory with alanine transaminase, and with liver fibrosis/cirrhosis.
RESULTS: We retrieved data from 1,885 adults on NA treatment (median follow-up 6.2 years, IQR 3.7-9.3 years), with 21,691 VL measurements (median 10 per patient, IQR 5-17). Five VL classes were identified from the derivation cohort (n = 1,367, discrimination: 0.93, entropy: 0.90): class 1 'long term suppression' (n = 827, 60.5%), class 2 'timely virological suppression' (n = 254, 18.6%), class 3 'persistent moderate viraemia' (n = 140, 10.2%), class 4 'persistent high-level viraemia' (n = 44, 3.2%), and class 5 'slow virological suppression' (n = 102, 7.5%). The model demonstrated a discrimination of 0.93 and entropy of 0.88 for the validation cohort (n = 518). Alanine transaminase decreased variably over time in VL-suppressed groups (classes 1, 2, 5; all p <0.001), but did not significantly improve in those with persistent viraemia (classes 3, 4). Patients in class 5 had twofold increased hazards of fibrosis/cirrhosis compared with class 1 (adjusted hazard ratio, 2.00; 95% CI, 1.33-3.02).
CONCLUSIONS: Heterogeneity exists in virological response to NA therapy in CHB patients, with over 20% showing potentially suboptimal responses. Slow virological suppression is associated with liver disease progression.
IMPACT AND IMPLICATIONS: Treatment recommendations for people living with chronic hepatitis B virus (HBV) infection are becoming less stringent, meaning that more of the population will be eligible to receive therapy with nucleos(t)ide analogue agents. We explored outcomes of HBV treatment in a large UK dataset, describing different responses to treatment, and showing that the viral load is not completely suppressed after 1 year in about one in five cases, associated with an increased risk of liver complications. As treatment is rolled out more widely, patients and clinicians need to be aware of the potential for incomplete virologic responses. The findings can support the identification of high-risk individuals, improve early fibrosis and cirrhosis prediction, guide monitoring and preventive interventions, and support public health elimination goals.}, }
@article {pmid39716198, year = {2024}, author = {Mendoza, JN and Prūse, B and Ciriaco, A and Mendoza, A and Ciriaco, H and Buen, C and Pua, JJ and Primavera, F and Mattalia, G and Sõukand, R}, title = {Fishery and ecology-related knowledge about plants among fishing communities along Laguna Lake, Philippines.}, journal = {Journal of ethnobiology and ethnomedicine}, volume = {20}, number = {1}, pages = {108}, pmid = {39716198}, issn = {1746-4269}, mesh = {*Fisheries ; Philippines ; *Ethnobotany ; Humans ; *Knowledge ; *Conservation of Natural Resources ; *Lakes ; Ecosystem ; Fishes ; Animals ; Ecology ; Female ; Male ; Middle Aged ; Adult ; Plants ; }, abstract = {BACKGROUND: Ethnobotanical knowledge about plant roles in fisheries is crucial for sustainable resource management. Local ecological knowledge helps understand dynamics of the lake ecosystem. Fishers use plants based on availability and characteristics while adapting to the changes in the environment. Studying fishery related uses of plants and algae and the challenges interconnected with them from local perspectives can provide insights into their beneficial uses and impacts to the ecosystem.
METHODS: The study investigates the botanical knowledge of three fishing villages in Laguna Lake or Laguna de Bay (LB), Philippines, including Buhangin, Sampiruhan, and Mabato-Azufre, each with varying degrees of industrialization. The ethnobotanical study, which gathered 27 interviews between June 2022 and July 2024, included plant collection with the help of local collaborators, including local fishers as research guides.
RESULTS: Fishers in LB highlighted positive and negative plant-fishing interactions. The most frequently mentioned plant applications were fish habitat and fish hiding places. Fish food, spawning sites, conservation, and a number of challenges such as navigational concerns and aquaculture fish deaths had been previously reported in local use reports. The remaining observations provide new insights into plant-fishing interactions, including indicators of food quality and food sources for fish, the decrease in the action of waves, and how plants help in improving the quality of the water.
CONCLUSION: These results highlight that the knowledge of fishers regarding the ecosystem in which they conduct their fishing activities provides baseline information about the positive and negative relationships between plants and fishing activities in the region, which is vital for further understanding its biodiversity and ecosystem interactions. It is crucial to consider fisher knowledge and involve them as equal partners in conservation efforts of LB.}, }
@article {pmid39716000, year = {2025}, author = {Chunduri, JR and Sagar, SP}, title = {Insect Brain Proteomics: A Case Study of Periplaneta americana.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2884}, number = {}, pages = {99-118}, pmid = {39716000}, issn = {1940-6029}, mesh = {Animals ; *Periplaneta/metabolism ; *Proteomics/methods ; *Brain/metabolism ; *Insect Proteins/metabolism/analysis ; *Proteome ; Chromatography, Liquid/methods ; Mass Spectrometry/methods ; Computational Biology/methods ; }, abstract = {Insects are known invertebrate species with economic, ecological, pathological, and medicinal value, as well as closely associated with human populations. Entomophagy and entomotherapy are future promising prospects largely attributable to the abundant availability, high protein content, and climatic sustainability of insects. In particular, the insect brain is an important system with a secluded, compact, and protective exoskeleton. It is immunologically privileged and capable of producing a robust immune response against pathogens. It is also a source of materials that initiate key activity throughout the body. Proteomic interrogation of Periplaneta americana enables understanding the role of this insect in the fields of food and pharmacology. Proximate analyses of P. americana highlights its richness in proteins. Here we perform a simple proteomic analysis to study the brain proteome of P. americana. The processes applied during the study include gel-based isolation and separation of proteins, followed by NanoLC-MS (Orbitrap) analyses and bioinformatic interrogation of the data. The results demonstrated that this insect proteome comprises antimicrobial proteins, allergens, and proteins required for metabolic processes.}, }
@article {pmid39713561, year = {2024}, author = {Blair, ME and Noguera-Urbano, EA and Ochoa-Quintero, JM and Paz, A and Lopez-Gallego, C and Echeverry-Galvis, MÁ and Zuloaga, J and Rodríguez, P and Lemus-Mejia, L and Ersts, P and López-Lozano, DF and Aiello-Lammens, ME and Arango, HM and Buitrago, L and Chang Triguero, S and Cruz-Rodríguez, CA and Díaz-Nieto, JF and Escobar, D and Grisales-Betancur, V and Johnson, BA and Kass, JM and Londoño-Murcia, MC and Merow, C and Muñoz-Rodríguez, CJ and Olaya-Rodríguez, MH and Parra, JL and Pinilla-Buitrago, GE and Roach, NS and Rojas-Soto, O and Roncancio-Duque, N and Suárez-Valencia, E and Urbina-Cardona, JN and Velásquez-Tibatá, J and Zapata-Martinez, CA and Anderson, RP}, title = {Software codesign between end users and developers to enhance utility for biodiversity conservation.}, journal = {Bioscience}, volume = {74}, number = {12}, pages = {867-873}, pmid = {39713561}, issn = {0006-3568}, abstract = {Creating software tools that address the needs of a wide range of decision-makers requires the inclusion of differing perspectives throughout the development process. Software tools for biodiversity conservation often fall short in this regard, partly because broad decision-maker needs may exceed the toolkits of single research groups or even institutions. We show that participatory, collaborative codesign enhances the utility of software tools for better decision-making in biodiversity conservation planning, as demonstrated by our experiences developing a set of integrated tools in Colombia. Specifically, we undertook an interdisciplinary, multi-institutional collaboration of ecological modelers, software engineers, and a diverse profile of potential end users, including decision-makers, conservation practitioners, and biodiversity experts. We leveraged and modified common paradigms of software production, including codesign and agile development, to facilitate collaboration through all stages (including conceptualization, development, testing, and feedback) to ensure the accessibility and applicability of the new tools to inform decision-making for biodiversity conservation planning.}, }
@article {pmid39710433, year = {2024}, author = {Yuan, H and Hicks, P and Ahmadian, M and Johnson, KA and Valtadoros, L and Krishnan, A}, title = {Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39710433}, issn = {1477-4054}, support = {2328140//National Science Foundation/ ; }, mesh = {*Metadata ; *Natural Language Processing ; *Machine Learning ; Humans ; Computational Biology/methods ; Proteomics/methods ; Vocabulary, Controlled ; }, abstract = {Reusing massive collections of publicly available biomedical data can significantly impact knowledge discovery. However, these public samples and studies are typically described using unstructured plain text, hindering the findability and further reuse of the data. To combat this problem, we propose txt2onto 2.0, a general-purpose method based on natural language processing and machine learning for annotating biomedical unstructured metadata to controlled vocabularies of diseases and tissues. Compared to the previous version (txt2onto 1.0), which uses numerical embeddings as features, this new version uses words as features, resulting in improved interpretability and performance, especially when few positive training instances are available. Txt2onto 2.0 uses embeddings from a large language model during prediction to deal with unseen-yet-relevant words related to each disease and tissue term being predicted from the input text, thereby explaining the basis of every annotation. We demonstrate the generalizability of txt2onto 2.0 by accurately predicting disease annotations for studies from independent datasets, using proteomics and clinical trials as examples. Overall, our approach can annotate biomedical text regardless of experimental types or sources. Code, data, and trained models are available at https://github.com/krishnanlab/txt2onto2.0.}, }
@article {pmid39709508, year = {2024}, author = {De Wint, FC and Nicholson, S and Koid, QQ and Zahra, S and Chestney-Claassen, G and Seelan, JSS and Xie, J and Xing, S and Fayle, TM and Haelewaters, D}, title = {Introducing a global database of entomopathogenic fungi and their host associations.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1418}, pmid = {39709508}, issn = {2052-4463}, support = {2023 Student Mobility Grant to F.C.D.W.//EC | Erasmus+/ ; Senior Postdoctoral Fellowship 1206024N to D.H.//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, mesh = {*Insecta/microbiology ; Animals ; *Databases, Factual ; *Hypocreales ; Host Specificity ; Biodiversity ; }, abstract = {Pathogens significantly influence natural and agricultural ecosystems, playing a crucial role in the regulation of species populations and maintaining biodiversity. Entomopathogenic fungi (EF), particularly within the Hypocreales order, exemplify understudied pathogens that infect insects and other arthropods globally. Despite their ecological importance, comprehensive data on EF host specificity and geographical distribution are lacking. To address this, we present EntomoFun 1.0, an open-access database centralizing global records of EF-insect associations in Hypocreales. This database includes 1,791 records detailing EF species, insect host taxa, countries of occurrence, life stages of hosts, and information sources. EntomoFun 1.0 is constructed based on 600 literature sources, as well as herbarium specimens of the Royal Botanical Gardens, Kew. This database is intended to test hypotheses, identify knowledge gaps, and stimulate future research. Contents of the EntomoFun 1.0 database are visualized with a global map, taxonomic chart, bipartite community network, and graphs.}, }
@article {pmid39709502, year = {2024}, author = {Jakobsson, M and Mohammad, R and Karlsson, M and Salas-Romero, S and Vacek, F and Heinze, F and Bringensparr, C and Castro, CF and Johnson, P and Kinney, J and Cardigos, S and Bogonko, M and Accettella, D and Amblas, D and An, L and Bohan, A and Brandt, A and Bünz, S and Canals, M and Casamor, JL and Coakley, B and Cornish, N and Danielson, S and Demarte, M and Di Franco, D and Dickson, ML and Dorschel, B and Dowdeswell, JA and Dreutter, S and Fremand, AC and Hall, JK and Hally, B and Holland, D and Hong, JK and Ivaldi, R and Knutz, PC and Krawczyk, DW and Kristofferson, Y and Lastras, G and Leck, C and Lucchi, RG and Masetti, G and Morlighem, M and Muchowski, J and Nielsen, T and Noormets, R and Plaza-Faverola, A and Prescott, MM and Purser, A and Rasmussen, TL and Rebesco, M and Rignot, E and Rysgaard, S and Silyakova, A and Snoeijs-Leijonmalm, P and Sørensen, A and Straneo, F and Sutherland, DA and Tate, AJ and Travaglini, P and Trenholm, N and van Wijk, E and Wallace, L and Willis, JK and Wood, M and Zimmermann, M and Zinglersen, KB and Mayer, L}, title = {The International Bathymetric Chart of the Arctic Ocean Version 5.0.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1420}, pmid = {39709502}, issn = {2052-4463}, abstract = {Knowledge about seafloor depth, or bathymetry, is crucial for various marine activities, including scientific research, offshore industry, safety of navigation, and ocean exploration. Mapping the central Arctic Ocean is challenging due to the presence of perennial sea ice, which limits data collection to icebreakers, submarines, and drifting ice stations. The International Bathymetric Chart of the Arctic Ocean (IBCAO) was initiated in 1997 with the goal of updating the Arctic Ocean bathymetric portrayal. The project team has since released four versions, each improving resolution and accuracy. Here, we present IBCAO Version 5.0, which offers a resolution four times as high as Version 4.0, with 100 × 100 m grid cells compared to 200 × 200 m. Over 25% of the Arctic Ocean is now mapped with individual depth soundings, based on a criterion that considers water depth. Version 5.0 also represents significant advancements in data compilation and computing techniques. Despite these improvements, challenges such as sea-ice cover and political dynamics still hinder comprehensive mapping.}, }
@article {pmid39707199, year = {2024}, author = {Zhang, M and Sun, Y and Lan, Y and Cheng, L and Lv, Z and Han, M and Yang, L}, title = {Multiomics joint analysis reveals the potential mechanism of differences in the taproot thickening between cultivated ginseng and mountain-cultivated ginseng.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1228}, pmid = {39707199}, issn = {1471-2164}, support = {20230204001YY//the Key Research and Development Projects of Jilin Province Science and Technology Development Plan/ ; 20200504002YY//the Major Projects of Jilin Province Science and Technology Development Plan/ ; CARS-21//the National Modern Agricultural Industrial Technology System Fund Project/ ; }, mesh = {*Panax/genetics/growth & development/metabolism ; *Plant Roots/genetics/growth & development/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Transcriptome ; Metabolomics ; Starch/metabolism ; Sucrose/metabolism ; Phenotype ; Genomics ; Multiomics ; }, abstract = {Panax ginseng is an important medicinal plant in China and is classified into two types: cultivated ginseng (CFCG) and mountain-cultivated ginseng (MCG). The two types of genetic varieties are the same, but the growth environments and management practices are different, resulting in substantial differences in their taproot morphology. Currently, there is a paucity of research on the internal mechanisms that regulate the phenotypic differences between cultivated ginseng and mountain-cultivated ginseng. In this study, we explored the potential mechanisms underlying their phenotypic differences using transcriptomic and metabolomic techniques. The results indicate that the taproot thickening of CFCG was significantly greater than that of MCG. Compared with MCG-4, MCG-10, and MCG-18, the diameters of the taproots of CFCG-4 increased by 158.96, 81.57, and 43.21%, respectively. Additionally, the contents of sucrose and starch in the taproot, as well as TRA and DHZR, were markedly elevated. Transcriptome analysis revealed that compared with MCG of different age groups, genes associated with starch and sucrose metabolism pathways (PgSUS1, PgSPS1, PgSPS3, and PgglgC1) were significantly upregulated in CFCG-4, whereas genes involved in the phenylpropanoid biosynthesis pathway (PgPER3, PgPER51, and PgPER12) were significantly downregulated in CFCG-4. This imbalance in the metabolic pathways suggests that these genes play crucial roles in ginseng taproot thickening. PgbHLH130 and PgARF18 may be key regulators of transcriptional changes in these pathways. These findings elucidate the molecular mechanisms governing ginseng taproot thickening, and have important implications for enhancing the overall quality and value of ginseng.}, }
@article {pmid39703500, year = {2024}, author = {Townsend, HA and Rosenberger, KJ and Vanderlinden, LA and Inamo, J and Zhang, F}, title = {Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1454263}, pmid = {39703500}, issn = {1664-3224}, mesh = {*Single-Cell Analysis/methods ; Humans ; *Genome-Wide Association Study ; Inflammation/genetics ; Arthritis, Rheumatoid/genetics/immunology ; Polymorphism, Single Nucleotide ; Genetic Predisposition to Disease ; Colitis, Ulcerative/genetics/immunology ; Algorithms ; Sequence Analysis, RNA/methods ; }, abstract = {BACKGROUND: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.
METHODS: We present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. First, we applied and compared the results of three recent algorithms, based on pathways (scGWAS), single-cell disease scores (scDRS), or both (scPagwas), according to accuracy/sensitivity and interpretability. While previous studies focused on coarse cell types, we used disease-specific, fine-grained single-cell atlases (183,742 and 228,211 cells) and GWAS data (Ns of 97,173 and 45,975) for rheumatoid arthritis (RA) and ulcerative colitis (UC). Second, given the lack of scRNA-seq for many diseases with GWAS, we further tested the tools' resolution limits by differentiating between similar diseases with only one fine-grained scRNA-seq atlas. Lastly, we provide a novel evaluation of noncoding SNP incorporation methods by testing which enabled the highest sensitivity/accuracy of known cell-state calls.
RESULTS: We first found that single-cell based tools scDRS and scPagwas called superior numbers of supported cell states that were overlooked by scGWAS. While scGWAS and scPagwas were advantageous for gene exploration, scDRS effectively accounted for batch effect and captured cellular heterogeneity of disease-relevance without single-cell genotyping. For noncoding SNP integration, we found a key trade-off between statistical power and confidence with positional (e.g. MAGMA) and non-positional approaches (e.g. chromatin-interaction, eQTL). Even when directly incorporating noncoding SNPs through 5' scRNA-seq measures of regulatory elements, non disease-specific atlases gave misleading results by not containing disease-tissue specific transcriptomic patterns. Despite this criticality of tissue-specific scRNA-seq, we showed that scDRS enabled deconvolution of two similar diseases with a single fine-grained scRNA-seq atlas and separate GWAS. Indeed, we identified supported and novel genetic-phenotype linkages separating RA and ankylosing spondylitis, and UC and crohn's disease. Overall, while noting evolving single-cell technologies, our study provides key findings for integrating expanding fine-grained scRNA-seq, GWAS, and noncoding SNP resources to unravel the complexities of inflammatory diseases.}, }
@article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).
METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.
RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.
CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, }
@article {pmid39700981, year = {2024}, author = {Wong, SY and Machado-de-Lima, NM and Wilkins, D and Zhang, E and Ferrari, BC}, title = {Fine-scale landscape heterogeneity drives microbial community structure at Robinson Ridge, East Antarctica.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177964}, doi = {10.1016/j.scitotenv.2024.177964}, pmid = {39700981}, issn = {1879-1026}, abstract = {Life at Robinson Ridge, located in the Windmill Islands region of East Antarctica, is susceptible to a changing climate. At this site, responses of the vegetation communities and moss-beds have been well researched, but corresponding information for microbial counterparts is still lacking. To bridge this knowledge gap, we established baseline data for monitoring the environmental drivers shaping the soil microbial community on the local 'hillslope' scale. Using triplicate 300-m long transects encompassing a hillslope with wind-exposed arid soils near the top, and snowmelt-sustained-moss beds at the bottom, we assessed the fine-scale heterogeneity of the soil environmental and microbial properties. Moist, low-lying, and vegetated soils exhibited higher soil fertility and unique biodiversity, with taxa adapted to thrive in moist conditions (i.e., Tardigrada, Phragmoplastophyta, Chloroflexi) and those that have previously demonstrated strong specificity for moss species (i.e., Fibrobacterota, Mucoromycota and Cyanobacteria) dominating. In contrast, elevated soils with limited moisture and nutrients were dominated by metabolically diverse phyla like Actinobacteriota and Ascomycota. Significant differences in microbial communities were observed at both hillslope (50-300 m) and fine spatial scales, as small as 0.1 m. Vertical heterogeneity was observed with higher abundances of Cyanobacteria and micro-algae in surfaces compared to subsoil, potentially indicating early biocrust formation. Stochastic and deterministic processes governing phylogenetic assembly were linked to soil positional groups and microbial domains rather than soil depth. Gradient Forest modeling identified critical environmental thresholds, such as ammonia, manganese, and sulphur, responsible for drastic community changes following level alterations. This reinforces the existence of strong niche preferences and distinct distribution patterns within the local microbial communities. This study highlights the need for finer-scale investigations considering site topography to better understand the relationship between environmental drivers and local microbiota. Ultimately, these insights enable us to understand environmental drivers and predict Antarctic ecosystem responses, helping safeguard this fragile environment.}, }
@article {pmid39700412, year = {2024}, author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL}, title = {The Naïve Bayes Classifier ++ for Metagenomic Taxonomic Classification-Query Evaluation.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae743}, pmid = {39700412}, issn = {1367-4811}, abstract = {MOTIVATION: This study examines the query performance of the NBC ++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC ++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.
RESULTS: NBC ++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC ++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC ++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.
AVAILABILITY: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, and databases are available at Zenodo records #11657719 and #11643985.}, }
@article {pmid39695923, year = {2024}, author = {Zhang, Z and Li, Q and Li, H and Wei, S and Yu, W and Peng, Z and Wei, F and Zhou, W}, title = {Integrative multi-omics analysis reveals the contribution of neoVTX genes to venom diversity of Synanceia verrucosa.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1210}, pmid = {39695923}, issn = {1471-2164}, support = {2023YFF1304900//Ministry of Science and Technology of the People's Republic of China/ ; 2024A1515013196//Science and Technology Department of Guangdong Province/ ; SLYJ2023B4004//Guangdong Forestry Administration/ ; GML2020GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; GML2022GD0804//PI Project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 32222014//National Natural Science Foundation of China/ ; 2021YFF0502804//Ministry of Science and Technology of China/ ; }, mesh = {Animals ; *Transcriptome ; Fish Venoms/genetics/chemistry ; Genomics/methods ; Proteomics ; Proteome ; Alternative Splicing ; Fishes/genetics ; Phylogeny ; Gene Expression Profiling ; Multiomics ; }, abstract = {BACKGROUND: Animal venom systems are considered as valuable model for investigating the molecular mechanisms underlying phenotypic evolution. Stonefish are the most venomous and dangerous fish because of severe human envenomation and occasionally fatalities, whereas the genomic background of their venom has not been fully explored compared with that in other venomous animals.
RESULTS: In this study, we followed modern venomic pipelines to decode the Synanceia verrucosa venom components. A catalog of 478 toxin genes was annotated based on our assembled chromosome-level genome. Integrative analysis of the high-quality genome, the transcriptome of the venom gland, and the proteome of crude venom revealed mechanisms underlying the venom complexity in S. verrucosa. Six tandem-duplicated neoVTX subunit genes were identified as the major source for the neoVTX protein production. Further isoform sequencing revealed massive alternative splicing events with a total of 411 isoforms demonstrated by the six genes, which further contributed to the venom diversity. We then characterized 12 dominantly expressed toxin genes in the venom gland, and 11 of which were evidenced to produce the venom protein components, with the neoVTX proteins as the most abundant. Other major venom proteins included a presumed CRVP, Kuntiz-type serine protease inhibitor, calglandulin protein, and hyaluronidase. Besides, a few of highly abundant non-toxin proteins were also characterized and they were hypothesized to function in housekeeping or hemostasis maintaining roles in the venom gland. Notably, gastrotropin like non-toxin proteins were the second highest abundant proteins in the venom, which have not been reported in other venomous animals and contribute to the unique venom properties of S. verrucosa.
CONCLUSIONS: The results identified the major venom composition of S. verrucosa, and highlighted the contribution of neoVTX genes to the diversity of venom composition through tandem-duplication and alternative splicing. The diverse neoVTX proteins in the venom as lethal particles are important for understanding the adaptive evolution of S. verrucosa. Further functional studies are encouraged to exploit the venom components of S. verrucosa for pharmaceutical innovation.}, }
@article {pmid39695260, year = {2024}, author = {Ma, X and Zheng, G and Xu, C and Moskal, LM and Gong, P and Guo, Q and Huang, H and Li, X and Liang, X and Pang, Y and Wang, C and Xie, H and Yu, B and Zhao, B and Zhou, Y}, title = {A global product of 150-m urban building height based on spaceborne lidar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1387}, pmid = {39695260}, issn = {2052-4463}, support = {42171340//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Urban building height, as a fundamental 3D urban structural feature, has far-reaching applications. However, creating readily available datasets of recent urban building heights with fine spatial resolutions and global coverage remains a challenging task. Here, we provide a 150-m global urban building heights dataset around 2020 by combining the spaceborne lidar (Global Ecosystem Dynamics Investigation, GEDI), multi-sourced data (Landsat-8, Sentinel-2, and Sentinel-1), and topographic data. The validation results revealed that the GEDI-estimated building height samples were effective compared to the reference data (Pearson's r = 0.81, RMSE = 3.58 m). The mapping product also demonstrated good performance, as indicated by its strong correlation with the reference data (Pearson's r = 0.71, RMSE = 4.73 m). Compared with the currently existing datasets, it holds the ability to provide a spatial resolution (150 m) with a great level of inherent details about the spatial heterogeneity and flexibility of updating using the GEDI samples as inputs. This product will boost future urban studies across many fields, including environmental, ecological, and social sciences.}, }
@article {pmid39694720, year = {2024}, author = {Reynolds, SA and Beery, S and Burgess, N and Burgman, M and Butchart, SHM and Cooke, SJ and Coomes, D and Danielsen, F and Di Minin, E and Durán, AP and Gassert, F and Hinsley, A and Jaffer, S and Jones, JPG and Li, BV and Mac Aodha, O and Madhavapeddy, A and O'Donnell, SAL and Oxbury, WM and Peck, L and Pettorelli, N and Rodríguez, JP and Shuckburgh, E and Strassburg, B and Yamashita, H and Miao, Z and Sutherland, WJ}, title = {The potential for AI to revolutionize conservation: a horizon scan.}, journal = {Trends in ecology & evolution}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tree.2024.11.013}, pmid = {39694720}, issn = {1872-8383}, abstract = {Artificial Intelligence (AI) is an emerging tool that could be leveraged to identify the effective conservation solutions demanded by the urgent biodiversity crisis. We present the results of our horizon scan of AI applications likely to significantly benefit biological conservation. An international panel of conservation scientists and AI experts identified 21 key ideas. These included species recognition to uncover 'dark diversity', multimodal models to improve biodiversity loss predictions, monitoring wildlife trade, and addressing human-wildlife conflict. We consider the potential negative impacts of AI adoption, such as AI colonialism and loss of essential conservation skills, and suggest how the conservation field might adapt to harness the benefits of AI while mitigating its risks.}, }
@article {pmid39692459, year = {2024}, author = {Shitindo, M}, title = {Interactions between wild pigs and the spread of disease.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39692459}, issn = {2050-084X}, mesh = {Animals ; *Animals, Wild ; Swine ; Swine Diseases ; Geographic Information Systems ; Humans ; }, abstract = {Tracking wild pigs with GPS devices reveals how their social interactions could influence the spread of disease, offering new strategies for protecting agriculture, wildlife, and human health.}, }
@article {pmid39691468, year = {2024}, author = {Winders, S and Yoo, L and Heitkemper, M and Kamp, K}, title = {Multilevel Factors and Sleep in Adults With Inflammatory Bowel Disease: A Qualitative Study.}, journal = {Crohn's & colitis 360}, volume = {6}, number = {4}, pages = {otae075}, pmid = {39691468}, issn = {2631-827X}, abstract = {BACKGROUND: This study aimed to describe the patient-reported factors that impact sleep among individuals with inflammatory bowel disease (IBD), aligning with the Social Ecological Model of Sleep. This addresses the gap in IBD sleep research, which predominantly focuses on individual-level factors and their impact on sleep.
METHODS: Adults (ages 18-65) with IBD were recruited online through ResearchMatch in June 2023. Participants filled out survey questions on their demographic characteristics, health history, sleep, and IBD-related symptoms. Content analysis was conducted on 2 open-ended questions about factors that impacted their sleep.
RESULTS: This analysis included 163 adults with IBD (M = 39 years of age, 76.7% White, 91.4% non-Hispanic or Latino, 66.9% female, and 83.4% active IBD) who answered open-ended questions with comments about their sleep. Most participants indicated an individual-level factor impacted their sleep quality (85.3%, n = 139), categorized into 5 subthemes: Mental health, health, behavior and choices, physiology, and attitudes. Additionally, participants (43.6%, n = 71) mentioned social-level factors divided into 7 subthemes: Family, work, home, neighborhood, social network, and school. A smaller group of participants (17.2%, n = 28) mentioned societal-level factors designated into 4 subthemes: Natural environment and geography, technology, 24/7 society, and economics.
CONCLUSIONS: This study highlights the need for tailored sleep interventions for those with IBD that consider not only disease activity but also mental health, family, work, and the natural environment. IBD clinics should prioritize sleep health using an interdisciplinary approach to holistically address the unique needs of those with IBD.}, }
@article {pmid39689854, year = {2024}, author = {Radice, VZ and Hernández-Agreda, A and Pérez-Rosales, G and Booker, R and Bellworthy, J and Broadribb, M and Carpenter, GE and Diaz, C and Eckert, RJ and Foster, NL and Gijsbers, JC and Gress, E and Laverick, JH and Micaroni, V and Pierotti, M and Rouzé, H and Stevenson, A and Sturm, AB and Bongaerts, P}, title = {Recent trends and biases in mesophotic ecosystem research.}, journal = {Biology letters}, volume = {20}, number = {12}, pages = {20240465}, pmid = {39689854}, issn = {1744-957X}, mesh = {*Ecosystem ; Animals ; Oceans and Seas ; Research/trends ; Anthozoa/physiology ; Bias ; Databases, Factual ; }, abstract = {Mesophotic ecosystems (approx. 30-150 m) represent a significant proportion of the world's oceans yet have long remained understudied due to challenges in accessing these deeper depths. Owing to advances in underwater technologies and a growing scientific and management interest, there has been a major expansion in research of both (sub)tropical mesophotic coral ecosystems and temperate mesophotic ecosystems. Here, we characterize the recent global trends in mesophotic research through an updated release of the 'mesophotic.org' database (www.mesophotic.org) where we reviewed and catalogued 1500 scientific publications. In doing so, we shed light on four major research biases: a gross imbalance in (a) the geographical spread of research efforts, differences in (b) the focal depth range and (c) research fields associated with study organisms and research platforms, and (d) the lack of temporal studies. Overall, we are optimistic about the future of mesophotic research and hope that by highlighting current trends and imbalances, we can raise awareness and stimulate discussion on the future directions of this emerging field.}, }
@article {pmid39689059, year = {2024}, author = {Bernadou, A and Jeanson, R}, title = {Randomness as a driver of inactivity in social groups.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012668}, pmid = {39689059}, issn = {1553-7358}, mesh = {Animals ; *Ants/physiology ; *Social Behavior ; Behavior, Animal/physiology ; Models, Biological ; Bees/physiology ; Computational Biology ; Computer Simulation ; Social Group ; }, abstract = {Social insects, such as ants and bees, are known for their highly efficient and structured colonies. Division of labour, in which each member of the colony has a specific role, is considered to be one major driver of their ecological success. However, empirical evidence has accumulated showing that many workers, sometimes more than half, remain idle in insect societies. Several hypotheses have been put forward to explain these patterns, but none provides a consensual explanation. Task specialisation exploits inter-individual variations, which are mainly influenced by genetic factors beyond the control of the colony. As a result, individuals may also differ in the efficiency with which they perform tasks. In this context, we aimed to test the hypothesis that colonies generate a large number of individuals in order to recruit only the most efficient to perform tasks, at the cost of producing and maintaining a fraction of workers that remain inactive. We developed a model to explore the conditions under which variations in the scaling of workers' production and maintenance costs, along with activity costs, allow colonies to sustain a fraction of inactive workers. We sampled individual performances according to different random distributions in order to simulate the variability associated with worker efficiency. Our results show that the inactivity of part of the workforce can be beneficial for a wide range of parameters if it allows colonies to select the most efficient workers. In decentralised systems such as insect societies, we suggest that inactivity is a by-product of the random processes associated with the generation of individuals whose performance levels cannot be controlled.}, }
@article {pmid39688289, year = {2024}, author = {Bao, Y and Jia, F and Geng, Y and Song, G and Xu, R and Wang, H and Mu, Y and Tong, HHY and Zhang, F and Guo, J}, title = {Uncovering the Differed Susceptibility of Fusarium oxysporum (Fo32931 and FocII5) to Fungicide Phenamacril: From Computational and Experimental Perspectives.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07865}, pmid = {39688289}, issn = {1520-5118}, abstract = {Fo32931 and FoCII5 are two subtypes of Fusarium oxysporum (Fo), a pathogenic filamentous fungus. Phenamacril (PHA), a Fusarium-specific fungicide that targets myosin I, exhibits significant hyphal growth inhibition in Fo32931 but shows weak resistance in FocII5, despite only two amino acid differences in the PHA-binding pocket of myosin I. In this study, we aim to elucidate the molecular basis for the differential sensitivity ofF. oxysporum myosin I variants (FoMyoI[32931] and FoMyoI[cII5]) to phenamacril through computational methods and biochemical validation. The results suggest that phenamacril functions as an allosteric inhibitor for FoMyoI[32931], inhibiting the large oscillation of the converter lever domain (CLD) upon ATP binding and promoting the opening of the outer cleft, further impairing protein function. PHA significantly reduced the coupling between the CLD, especially the converter, and the catalytic center, diminishing the response of the CLD to the motor domain in FoMyoI[32931]. From the residue mutation experiment, we found that the S418T substitution in FoMyoI[cII5] is the key to the reduced phenamacril sensitivity of FocII5. According to the microscale thermophoresis (MST) assay and pocket conformation analysis, the S418T mutation disturbs the orientation of pocket residues, especially Lys537, leading to a looser pocket and reduced interaction between Lys537 and phenamacril, which lowers the binding affinity of FoMyoI[cII5] for phenamacril. These findings provide deeper insights into the reasons for the lower sensitivity of FoCII5 to phenamacril from both molecular and structural perspectives and will also guide the design of novel inhibitors against resistant Fusarium spp., like FoCII5.}, }
@article {pmid39684926, year = {2024}, author = {Liu, R and Zhang, P and Bai, J and Zhong, Z and Shan, Y and Cheng, Z and Zhang, Q and Guo, Q and Zhang, H and Zhang, B}, title = {Integrated Transcriptomic and Proteomic Analyses of Antler Growth and Ossification Mechanisms.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684926}, issn = {1422-0067}, support = {23CB063 and 24CE-BGS-09//Beijing Academy of Science and Technology Financial Support Projects/ ; }, mesh = {*Antlers/growth & development/metabolism ; Animals ; *Osteogenesis/genetics ; *Deer/genetics/growth & development ; *Transcriptome ; *Proteomics/methods ; Proteome/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; }, abstract = {Antlers are the sole mammalian organs capable of continuous regeneration. This distinctive feature has evolved into various biomedical models. Research on mechanisms of antler growth, development, and ossification provides valuable insights for limb regeneration, cartilage-related diseases, and cancer mechanisms. Here, ribonucleic acid sequencing (RNA-seq) and four-dimensional data-independent acquisition (4D DIA) technologies were employed to examine gene and protein expression differences among four tissue layers of the Chinese milu deer antler: reserve mesenchyme (RM), precartilage (PC), transition zone (TZ), cartilage (CA). Overall, 4611 differentially expressed genes (DEGs) and 2388 differentially expressed proteins (DEPs) were identified in the transcriptome and proteome, respectively. Among the 828 DEGs common to both omics approaches, genes from the collagen, integrin, and solute carrier families, and signaling molecules were emphasized for their roles in the regulation of antler growth, development, and ossification. Bioinformatics analysis revealed that in addition to being regulated by vascular and nerve regeneration pathways, antler growth and development are significantly influenced by numerous cancer-related signaling pathways. This indicates that antler growth mechanisms may be similar to those of cancer cell proliferation and development. This study lays a foundation for future research on the mechanisms underlying the rapid growth and ossification of antlers.}, }
@article {pmid39684378, year = {2024}, author = {Zhang, KL and Leng, YN and Hao, RR and Zhang, WY and Li, HF and Chen, MX and Zhu, FY}, title = {Adaptation of High-Altitude Plants to Harsh Environments: Application of Phenotypic-Variation-Related Methods and Multi-Omics Techniques.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684378}, issn = {1422-0067}, support = {KYCX24_1376//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; 2023ZD0405602//STI 2030－Major Projects/ ; CX (21)2023//Jiangsu Agricultural Science and Technology Innovation Fund/ ; BK20240668//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Altitude ; *Metabolomics/methods ; *Plants/metabolism/genetics ; *Proteomics/methods ; *Adaptation, Physiological ; *Genomics/methods ; *Phenotype ; Plant Physiological Phenomena ; Acclimatization ; Transcriptome ; Multiomics ; }, abstract = {High-altitude plants face extreme environments such as low temperature, low oxygen, low nutrient levels, and strong ultraviolet radiation, causing them to adopt complex adaptation mechanisms. Phenotypic variation is the core manifestation of ecological adaptation and evolution. Many plants have developed a series of adaptive strategies through long-term natural selection and evolution, enabling them to survive and reproduce under such harsh conditions. This article reviews the techniques and methods used in recent years to study the adaptive evolution of high-altitude plants, including transplantation techniques, genomics, transcriptomics, proteomics, and metabolomics techniques, and their applications in high-altitude plant adaptive evolution. Transplantation technology focuses on phenotypic variation, which refers to natural variations in morphological, physiological, and biochemical characteristics, exploring their key roles in nutrient utilization, photosynthesis optimization, and stress-resistance protection. Multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revealed genes, regulatory pathways, and metabolic networks associated with phenotypic variations at the genetic and molecular levels. At the same time, the limitations and deficiencies of current technologies used to study plant adaptation to high-altitude environments were discussed. In addition, we propose future improvements to existing technologies and advocate for the integration of different technologies at multiple levels to study the molecular mechanisms of plant adaptation to high-altitude environments, thus providing insights for future research in this field.}, }
@article {pmid39683090, year = {2024}, author = {Chaligava, O and Zinicovscaia, I and Peshkova, A and Yushin, N and Frontasyeva, M and Vergel, K and Nurkassimova, M and Cepoi, L}, title = {Major and Trace Airborne Elements and Ecological Risk Assessment: Georgia Moss Survey 2019-2023.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {23}, pages = {}, pmid = {39683090}, issn = {2223-7747}, abstract = {The study, carried out as part of the International Cooperative Program on Effects of Air Pollution on Natural Vegetation and Crops, involved collecting 95 moss samples across the territory of Georgia during the period from 2019 to 2023. Primarily samples of Hypnum cupressiforme were selected, with supplementary samples of Abietinella abietina, Pleurozium schreberi, and Hylocomium splendens in cases of the former's absence. The content of 14 elements (Al, Ba, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, S, Sr, V, and Zn) was detected using Inductively Coupled Plasma Atomic Emission Spectroscopy (ICP-AES), while the Hg content was determined using a Direct Mercury Analyzer. To identify any relationships between chemical elements and to depict their sources, multivariate statistics was applied. Principal component analysis identified three main components: PC1 (geogenic, 43.4%), PC2 (anthropogenic, 13.3%), and PC3 (local anomalies, 8.5%). The results were compared with the first moss survey conducted in Georgia in the period from 2014 to 2017, offering insights into temporal trends of air quality. Utilizing GIS, a spatial map illustrating pollution levels across Georgia, based on the Pollution Load Index, was generated. The Potential Environmental Risk Index emphasized significant risks associated with mercury and cadmium at several locations. The study highlights the utility of moss biomonitoring in assessing air pollution and identifying hotspots of contamination. The findings from this study could be beneficial for future biomonitoring research in areas with varying physical and geographical conditions.}, }
@article {pmid39679384, year = {2024}, author = {Khosravi, M and Mojtabaeian, SM and Sarvestani, MA}, title = {A Systematic Review on the Outcomes of Climate Change in the Middle-Eastern Countries: The Catastrophes of Yemen and Syria.}, journal = {Environmental health insights}, volume = {18}, number = {}, pages = {11786302241302270}, pmid = {39679384}, issn = {1178-6302}, abstract = {The Middle East is facing serious climate change challenges, rendering it as one of the most affected regions worldwide. This paper aimed to investigate the outcomes of climate change in the Middle East. In 2024, a qualitative study was conducted employing a methodology that integrated systematic review for data collection and thematic analysis for data analysis. Such integration of the approaches provided valuable insights into the findings within the literature in a comprehensive and categorized format. PubMed, Scopus, ProQuest, and the Cochrane Database of Systematic Reviews were searched for relevant studies published between 2000 and 2024. The quality of these studies was assessed using the AACODS (Accuracy, Coverage, Objectivity, Date, Significance) checklist. The data extracted from the included studies underwent a thematic analysis utilizing Braun and Clarke's methodology. After completing the screening process, a total of 93 papers were deemed suitable for inclusion in the study. The quality assessment of these selected studies demonstrated a notably high standard, particularly in terms of authority, accuracy, coverage, objectivity, and significance. Moreover, minimal levels of bias were observed within the included studies. Subsequent thematic analysis of the findings from the systematic review identified 6 overarching themes: "Human Health Outcomes," "Animal Health Outcomes," "Plant Health Outcomes," "Ecological Outcomes," "Economic Outcomes," and "Political Outcomes." The study revealed ecological outcomes as the most prevalent consequences of climate change in the Middle East, including alterations in habitat distribution, temperature increase, water scarcity, and more. The outcomes seemed to be interconnected, exacerbating each other. Yemen and Syria had faced severe consequences, leading to political unrest and humanitarian crises in which Yemen ranking among the most water-stressed nations globally, while Syria contending with millions of displaced individuals living in dire conditions.}, }
@article {pmid39675288, year = {2024}, author = {Mu, X and Chen, C and Fan, Q and Zhang, W and Liu, F and Guo, J and Qi, W and Liu, H}, title = {Removal and ecological impact of sulfamethoxazole and N-acetyl sulfamethoxazole in mesocosmic wetlands dominated by submerged plants: Plant tolerance, microbial response, and nitrogen transformation.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178034}, doi = {10.1016/j.scitotenv.2024.178034}, pmid = {39675288}, issn = {1879-1026}, abstract = {Sulfamethoxazole (SMX) and its human metabolite N-acetylsulfamethoxazole (N-SMX) are frequently detected in aquatic environments, posing potential threats to freshwater ecosystem health. Constructed wetlands are pivotal for wastewater treatment, with plant species serving as key determinants of pollutant removal efficiency. In this study, wetlands dominated by three submerged plants (Myriophyllum verticillatum, Vallisneria spiralis, Hydrilla verticillata) were respectively constructed to investigate the removal of SMX and N-SMX, and the impact on wetland ecology regarding plant tolerance, microbial response, and nitrogen transformation. Results showed that wetlands removed N-SMX (82.3-99.8 %) more effectively than SMX (54.3-80.2 %), with the wetland dominated by Myriophyllum verticillatum showing the highest removal efficiency. However, high concentrations (5 mg/L) of SMX and N-SMX significantly reduced NH4[+]-N and TN removal (p < 0.05), accompanied by shifts in microbial communities, especially a decreased abundance of Proteobacteria and key nitrogen-transforming genes. A total of 22 different ARGs (antibiotic resistance genes) were detected. SMX significantly increased the relative abundance of sulfonamide resistance genes (sul1, sul2) (p < 0.05), while major denitrifying genera, such as Thiobacillus, which were not the primary hosts of these genes, showed a significant negative correlation with sul1 and sul2 (p < 0.05). This study provides a reference for ecological remediation of wetlands in response to antibiotic contamination.}, }
@article {pmid39656857, year = {2024}, author = {Alvarado, M and Gómez-Navajas, JA and Blázquez-Muñoz, MT and Gómez-Molero, E and Fernández-Sánchez, S and Eraso, E and Munro, CA and Valentín, E and Mateo, E and de Groot, PWJ}, title = {The good, the bad, and the hazardous: comparative genomic analysis unveils cell wall features in the pathogen Candidozyma auris typical for both baker's yeast and Candida.}, journal = {FEMS yeast research}, volume = {24}, number = {}, pages = {}, pmid = {39656857}, issn = {1567-1364}, support = {PID2020-117983RB-I00//Agencia Estatal de Investigación/ ; SBPLY/23/180225/000029//UCLM/ ; //European Regional Development Fund/ ; JDC2023-051226-I//European Social Fund Plus/ ; }, mesh = {*Cell Wall/metabolism ; *Saccharomyces cerevisiae/genetics/metabolism ; Computational Biology ; Genomics ; Candida auris/genetics/metabolism/drug effects ; beta-Glucans/metabolism ; Genome, Fungal ; Fungal Proteins/genetics/metabolism ; Glycosylphosphatidylinositols/metabolism/genetics ; Candida albicans/genetics/pathogenicity ; Candida/genetics/metabolism/pathogenicity ; }, abstract = {The drug-resistant pathogenic yeast Candidozyma auris (formerly named Candida auris) is considered a critical health problem of global importance. As the cell wall plays a crucial role in pathobiology, here we performed a detailed bioinformatic analysis of its biosynthesis in C. auris and related Candidozyma haemuli complex species using Candida albicans and Saccharomyces cerevisiae as references. Our data indicate that the cell wall architecture described for these reference yeasts is largely conserved in Candidozyma spp.; however, expansions or reductions in gene families point to subtle alterations, particularly with respect to β--1,3--glucan synthesis and remodeling, phosphomannosylation, β-mannosylation, and glycosylphosphatidylinositol (GPI) proteins. In several aspects, C. auris holds a position in between C. albicans and S. cerevisiae, consistent with being classified in a separate genus. Strikingly, among the identified putative GPI proteins in C. auris are adhesins typical for both Candida (Als and Hyr/Iff) and Saccharomyces (Flo11 and Flo5-like flocculins). Further, 26 putative C. auris GPI proteins lack homologs in Candida genus species. Phenotypic analysis of one such gene, QG37_05701, showed mild phenotypes implicating a role associated with cell wall β-1,3-glucan. Altogether, our study uncovered a wealth of information relevant for the pathogenicity of C. auris as well as targets for follow-up studies.}, }
@article {pmid39671449, year = {2024}, author = {Celiker, E and Woodrow, C and Guadayol, Ò and Davranoglou, LR and Schlepütz, CM and Mortimer, B and Taylor, GK and Humphries, S and Montealegre-Z, F}, title = {Mechanical network equivalence between the katydid and mammalian inner ears.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012641}, pmid = {39671449}, issn = {1553-7358}, mesh = {Animals ; *Ear, Inner/anatomy & histology/physiology ; *Mammals/physiology ; *Hearing/physiology ; Computer Simulation ; Insecta/physiology ; Computational Biology ; Models, Biological ; Cochlea/physiology/anatomy & histology ; X-Ray Microtomography ; }, abstract = {Mammalian hearing operates on three basic steps: 1) sound capturing, 2) impedance conversion, and 3) frequency analysis. While these canonical steps are vital for acoustic communication and survival in mammals, they are not unique to them. An equivalent mechanism has been described for katydids (Insecta), and it is unique to this group among invertebrates. The katydid inner ear resembles an uncoiled cochlea, and has a length less than 1 mm. Their inner ears contain the crista acustica, which holds tonotopically arranged sensory cells for frequency mapping via travelling waves. The crista acustica is located on a curved triangular surface formed by the dorsal wall of the ear canal. While empirical recordings show tonotopic vibrations in the katydid inner ear for frequency analysis, the biophysical mechanism leading to tonotopy remains elusive due to the small size and complexity of the hearing organ. In this study, robust numerical simulations are developed for an in silico investigation of this process. Simulations are based on the precise katydid inner ear geometry obtained by synchrotron-based micro-computed tomography, and empirically determined inner ear fluid properties for an accurate representation of the underlying mechanism. We demonstrate that the triangular structure below the hearing organ drives the tonotopy and travelling waves in the inner ear, and thus has an equivalent role to the mammalian basilar membrane. This reveals a stronger analogy between the inner ear basic mechanical networks of two organisms with ancient evolutionary differences and independent phylogenetic histories.}, }
@article {pmid39671336, year = {2024}, author = {Karim, AAJ and Mahmud, MZ and Khan, R}, title = {Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012654}, pmid = {39671336}, issn = {1553-7358}, mesh = {Animals ; *Culicidae/classification ; *Deep Learning ; *Computational Biology/methods ; Entomology/methods ; Mosquito Vectors/classification ; Humans ; Algorithms ; Neural Networks, Computer ; }, abstract = {Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by leveraging state-of-the-art vision transformers and open-set learning techniques. A novel framework has been introduced that integrates Transformer-based deep learning models with comprehensive data augmentation and preprocessing methods, enabling robust and precise identification of ten mosquito species. The Swin Transformer model achieves the best performance for traditional closed-set learning with 99.60% accuracy and 0.996 F1 score. The lightweight MobileViT technique attains an almost equivalent accuracy of 98.90% with significantly reduced parameters and model complexities. Next, the applied deep learning models' adaptability and generalizability in a static environment have been enhanced by using new classes of data samples during the inference stage that have not been included in the training set. The proposed framework's ability to handle unseen classes like insects similar to mosquitoes, even humans, through open-set learning further enhances its practical applicability employing the OpenMax technique and Weibull distribution. The traditional CNN model, Xception, outperforms the latest transformer with higher accuracy and F1 score for open-set learning. The study's findings highlight the transformative potential of advanced deep-learning architectures in entomology, providing a strong groundwork for future research and development in mosquito surveillance and vector control. The implications of this work extend beyond mosquito classification, offering valuable insights for broader ecological and environmental monitoring applications.}, }
@article {pmid39670410, year = {2025}, author = {Alipio, K and García-Colón, J and Boscarino, N and Fox, K}, title = {Indigenous Data Sovereignty, Circular Systems, and Solarpunk Solutions for a Sustainable Future.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {30}, number = {}, pages = {717-733}, pmid = {39670410}, issn = {2335-6936}, mesh = {*Artificial Intelligence ; *Computational Biology ; Humans ; Cloud Computing/statistics & numerical data ; Sustainable Development ; Indigenous Peoples/statistics & numerical data ; Conservation of Natural Resources ; }, abstract = {Recent advancements in Artificial Intelligence (AI) and data center infrastructure have brought the global cloud computing market to the forefront of conversations about sustainability and energy use. Current policy and infrastructure for data centers prioritize economic gain and resource extraction, inherently unsustainable models which generate massive amounts of energy and heat waste. Our team proposes the formation of policy around earth-friendly computation practices rooted in Indigenous models of circular systems of sustainability. By looking to alternative systems of sustainability rooted in Indigenous values of aloha 'āina, or love for the land, we find examples of traditional ecological knowledge (TEK) that can be imagined alongside Solarpunk visions for a more sustainable future. One in which technology works with the environment, reusing electronic waste (e-waste) and improving data life cycles.}, }
@article {pmid39664868, year = {2024}, author = {Boyes, D and Zilli, A and , and , and , and , and , and , and , }, title = {The genome sequence of the Grey Shoulder-knot, Lithophane ornitopus (Hufnagel, 1766).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {214}, pmid = {39664868}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lithophane ornitopus (the Grey Shoulder-knot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 508.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.33 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,397 protein coding genes.}, }
@article {pmid39664717, year = {2024}, author = {Baker, KS and Millerand, F}, title = {The Incremental Growth of Data Infrastructure in Ecology (1980-2020).}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70444}, pmid = {39664717}, issn = {2045-7758}, abstract = {After decades of growth, a research community's network information system and data repository were transformed to become a national data management office and a major element of data infrastructure for ecology and the environmental sciences. Developing functional data infrastructures is key to the support of ongoing Open Science and Open Data efforts. This example of data infrastructure growth contrasts with the top-down development typical of many digital initiatives. The trajectory of this network information system evolved within a collaborative, long-term ecological research community. This particular community is funded to conduct ecological research while collective data management is also carried out across its geographically dispersed study sites. From this longitudinal ethnography, we describe an Incremental Growth Model that includes a sequence of six relatively stable phases where each phase is initiated by a rapid response to a major pivotal event. Exploring these phases and the roles of data workers provides insight into major characteristics of digital growth. Further, a transformation in assumptions about data management is reported for each phase. Investigating the growth of a community information system over four decades as it becomes data infrastructure reveals details of its social, technical, and institutional dynamics. In addition to addressing how digital data infrastructure characteristics change, this study also considers when the growth of data infrastructure begins.}, }
@article {pmid39663400, year = {2024}, author = {Carter, KR and Cavaleri, MA and Atkin, OK and Bahar, NHA and Cheesman, AW and Choury, Z and Crous, KY and Doughty, CE and Dusenge, ME and Ely, KS and Evans, JR and Fonseca da Silva, J and Mau, AC and Medlyn, BE and Meir, P and Norby, RJ and Read, J and Reed, SC and Reich, PB and Rogers, A and Serbin, SP and Slot, M and Schwartz, EC and Tribuzy, ES and Uddling, J and Vårhammar, A and Walker, AP and Winter, K and Wood, TE and Wu, J}, title = {Photosynthetic responses to temperature across the tropics: a meta-analytic approach.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcae206}, pmid = {39663400}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: Tropical forests exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial biome. Yet, uncertainty in the projected carbon balance over the next century is roughly three-times greater for the tropics than other ecosystems. Our limited knowledge of tropical plant physiological responses, including photosynthetic, to climate change is a substantial source of uncertainty in our ability to forecast the global terrestrial carbon sink.
METHODS: We used a meta-analytic approach, focusing on tropical photosynthetic temperature responses, to address this knowledge gap. Our dataset, gleaned from 18 independent studies, included leaf-level light saturated photosynthetic (Asat) temperature responses from 108 woody species, with additional temperature parameters (35 species) and rates (250 species) of both maximum rates of electron transport (Jmax) and Rubisco carboxylation (Vcmax). We investigated how these parameters responded to mean annual temperature (MAT), temperature variability, aridity, and elevation, as well as also how responses differed among successional strategy, leaf habit, and light environment.
KEY RESULTS: Optimum temperatures for Asat (ToptA) and Jmax (ToptJ) increased with MAT but not for Vcmax (ToptV). Although photosynthetic rates were higher for "light" than "shaded" leaves, light conditions did not generate differences in temperature response parameters. ToptA did not differ with successional strategy, but early successional species had ~4 °C wider thermal niches than mid/late species. Semi-deciduous species had ~1 °C higher ToptA than broadleaf evergreen. Most global modeling efforts consider all tropical forests as a single "broadleaf evergreen" functional type, but our data show that tropical species with different leaf habits display distinct temperature responses that should be included in modeling efforts.
CONCLUSIONS: This novel research will inform modeling efforts to quantify tropical ecosystem carbon cycling and provide more accurate representations of how these key ecosystems will respond to altered temperature patterns in the face of climate warming.}, }
@article {pmid39660611, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39660611}, issn = {2050-084X}, support = {R01 AG075283/AG/NIA NIH HHS/United States ; 457837076//Deutsche Forschungsgemeinschaft/ ; W81XWH2020013//Congressionally Directed Medical Research Programs/ ; 1R01AG075283-01A1/NH/NIH HHS/United States ; }, mesh = {*Bacteriocins/pharmacology/genetics/metabolism ; *Enterobacteriaceae/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Gram-Negative Bacteria/drug effects/genetics ; Plant Diseases/microbiology ; Microbial Sensitivity Tests ; }, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered 12 previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella. Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e., Acinetobacter baumannii or Pseudomonas aeruginosa, providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, }
@article {pmid39657789, year = {2024}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae1115}, pmid = {39657789}, issn = {1362-4962}, support = {KICH1.LWV04.21.013//NWO/ ; 101000392//Horizon 2020/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; 547394769//German Research Foundation/ ; //University of Sydney/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; IM230100154//Australian Research Council Industry Fellowship/ ; //Hans Fischer Society/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; 101117891-MeDiSyn//ERC Starting/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; //Department of Biotechnology/ ; //National Agri-Food Biotechnology Institute/ ; 101087181//EU/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; 2021YFA0909500//National Key Research and Development Program of China/ ; 32170080//National Natural Science Foundation of China/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 21K06336//KAKENHI/ ; 21/07038-0//São Paulo Research Foundation/ ; VI.Veni.202.130//NWO Talent/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 222676//USDA Evans-Allen Research/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; //University of Illinois/ ; 802736//European Union Horizon 2020/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; //NWO Merian/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 101066127//European Union/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; K12 GM068524/GM/NIGMS NIH HHS/United States ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Alexander von Humboldt-Stiftung/ ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; NE/T010959/1//Signals in the Soil/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; 495740318//German Research Foundation/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; 101072485//European Union's Horizon/ ; //European Regional Development Fund/ ; 802736//European Union's Horizon 2020/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; //Swiss Federal Government/ ; PS00349981//Fulbright/ ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; DM60066//Italian Ministry of Research/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; NA22NOS4200050//NERRS/ ; BB/V005723/2//BBSRC/ ; 1347411//CONAHCYT/ ; T32GM136583/NH/NIH HHS/United States ; 101130799//European Union's Horizon/ ; CFB 2.0//Novo Nordisk Foundation/ ; //Basic Science Research Program/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; //Werner Siemens Foundation/ ; OCENW.XL21.XL21.088//NWO-XL/ ; DNRF137//Danish National Research Foundation/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; CBET-2032243//U.S. National Science Foundation/ ; //Delta Stewardship Council Delta Science Program/ ; //European Union's Horizon 2020 Research/ ; 852600//Innovation Program ERC St/ ; 101072485//European Union's Horizon Europe/ ; //Conahcyt Mexico International PhD Studentship/ ; //Strathclyde University Global Research Scholarship/ ; 3141-00013A//Innovation Fund Denmark/ ; K445/2022//Leibniz Association/ ; 23/01956-2//São Paulo Research Foundation/ ; DGE 2241144//NSF GRFP/ ; 024.004.014//MiCRop Consortium/ ; CF22-1239//Carlsberg Foundation/ ; 102022750//SINTEF/ ; 102029187//SEP AGREE/ ; 102024676-14//POS BIOINFO 2024/ ; 101106349//Marie Sklodowska-Curie/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //National Research Fund of Ukraine/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //German Academic Scholarship Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; //Department of Biotechnology/ ; //University Grants Commission/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; GNT2021638//National Health and Medical Research Council/ ; DP230102668//Australian Research Council Discovery Project/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 865738/ERC_/European Research Council/International ; T32-GM136629//Chemical-Biology Interface Training/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; 101099528//European Innovation Council/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; //Swedish Pharmaceutical Society PostDoc/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; //Saarland University/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; AUFF-E-2022-9-42//AUFF/ ; 101055020-COMMUNITY//ERC Advanced/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; 10.55776/P 34036//Austrian Science Fund/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39653494, year = {2024}, author = {Lee, HB and Nguyen, TTT and Noh, SJ and Kim, DH and Kang, KH and Kim, SJ and Kirk, PM and Avery, SV and Medina, A and Hallsworth, JE}, title = {Aspergillus ullungdoensis sp. nov., Penicillium jeongsukae sp. nov., and other fungi from Korea.}, journal = {Fungal biology}, volume = {128}, number = {8 Pt B}, pages = {2479-2492}, doi = {10.1016/j.funbio.2024.05.014}, pmid = {39653494}, issn = {1878-6146}, mesh = {Republic of Korea ; *Phylogeny ; *Penicillium/isolation & purification/classification/genetics ; DNA, Fungal/genetics ; Soil Microbiology ; Aspergillus/isolation & purification/classification/genetics ; Sequence Analysis, DNA ; Cluster Analysis ; DNA, Ribosomal Spacer/genetics/chemistry ; }, abstract = {Eurotiales fungi are thought to be distributed worldwide but there is a paucity of information about their occurrence on diverse substrates or hosts and at specific localities. Some of the Eurotiales, including Aspergillus and Penicillium species, produce an array of secondary metabolites of use for agricultural, medicinal, and pharmaceutical applications. Here, we carried out a survey of the Eurotiales in South Korea, focusing on soil, freshwater, and plants (dried persimmon fruits and seeds of Perilla frutescens, known commonly as shiso). We obtained 11 species that-based on morphology, physiology, and multi-locus (ITS, BenA, CaM, and RPB2) phylogenetic analyses-include two new species, Aspergillus ullungdoensis sp. nov. and Penicillium jeongsukae sp. nov., and nine species that were known, but previously not described in South Korea, Aspergillus aculeatinus, Aspergillus aurantiacoflavus, Aspergillus croceiaffinis, Aspergillus pseudoviridinutans, Aspergillus uvarum, Penicillium ferraniaense, Penicillium glaucoroseum, Penicillium sajarovii, and one, Penicillium charlesii, that was isolated from previously unknown host, woodlouse (Porcellio scaber). We believe that biodiversity survey and identifying new species can contribute to set a baseline for future changes in the context of humanitarian crises such as climate change.}, }
@article {pmid39652754, year = {2024}, author = {Pillay, R and Watson, JEM and Hansen, AJ and Burns, P and Virnig, ALS and Supples, C and Armenteras, D and González-Del-Pliego, P and Aragon-Osejo, J and A Jantz, P and Ervin, J and Goetz, SJ and Venter, O}, title = {Global rarity of high-integrity tropical rainforests for threatened and declining terrestrial vertebrates.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {51}, pages = {e2413325121}, pmid = {39652754}, issn = {1091-6490}, support = {NNX17AG51G/NASA/NASA/United States ; NNL15AA03/NASA/NASA/United States ; 80NSSC18K0338/NASA/NASA/United States ; }, mesh = {*Rainforest ; Animals ; *Biodiversity ; *Vertebrates/physiology ; *Conservation of Natural Resources/methods ; Tropical Climate ; Endangered Species ; Ecosystem ; }, abstract = {Structurally intact native forests free from major human pressures are vitally important habitats for the persistence of forest biodiversity. However, the extent of such high-integrity forest habitats remaining for biodiversity is unknown. Here, we quantify the amount of high-integrity tropical rainforests, as a fraction of total forest cover, within the geographic ranges of 16,396 species of terrestrial vertebrates worldwide. We found up to 90% of the humid tropical ranges of forest-dependent vertebrates was encompassed by forest cover. Concerningly, however, merely 25% of these remaining rainforests are of high integrity. Forest-dependent species that are threatened and declining and species with small geographic ranges have disproportionately low proportions of high-integrity forest habitat left. Our work brings much needed attention to the poor quality of much of the forest estate remaining for biodiversity across the humid tropics. The targeted preservation of the world's remaining high-integrity tropical rainforests that are currently unprotected is a critical conservation priority that may help alleviate the biodiversity crisis in these hyperdiverse and irreplaceable ecosystems. Enhanced efforts worldwide to preserve tropical rainforest integrity are essential to meet the targets of the Convention on Biological Diversity's 2022 Kunming-Montreal Global Biodiversity Framework which aims to achieve near zero loss of high biodiversity importance areas (including ecosystems of high integrity) by 2030.}, }
@article {pmid39649625, year = {2024}, author = {Boyes, D and Crowley, LC and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Broad-barred Knot-horn, Acrobasis consociella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {429}, pmid = {39649625}, issn = {2398-502X}, abstract = {We present a genome assembly from one female Acrobasis consociella (the Broad-barred Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 598.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.22 kilobases in length.}, }
@article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, }
@article {pmid39644634, year = {2024}, author = {Xie, Y and Guo, J and Fan, Q and Huang, S and Qi, W and Cao, X and Peng, J and Chen, Y and Chen, M}, title = {High-density sampling reveals the occurrence, levels and transport flux of 15 polycyclic aromatic hydrocarbons derivatives (PAHs-d) along the Yangtze River.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177907}, doi = {10.1016/j.scitotenv.2024.177907}, pmid = {39644634}, issn = {1879-1026}, abstract = {Polycyclic aromatic hydrocarbons derivatives (PAHs-d) have higher toxicity levels compared to its parent polycyclic aromatic hydrocarbons (PPAHs). Their partitioning in different media and large-scale transport patterns in rivers remain largely unknown. This study investigated the occurrence of 15 PAHs-d and 19 PPAHs in water and suspended particulate matter (SPM) of the Yangtze River between 2019 and 2020. The range of Σ15PAHs-d concentrations was 20.54 to 2010.03 ng·L[-1] in water and 0.62 to 29.80 μg·g[-1] in SPM. The primary PAHs-d components were 2,6-dimethylnaphthalene, 2-methylnaphthalene, and anthraquinone. The range of Σ19PPAHs concentrations in water and SPM was 34.89 to 739.53 ng·L[-1] and 0.37 to 204.62 μg·g[-1], respectively. And low-ring PAHs-d and PPAHs were more prevalent in water than SPM. Partitioning behaviors indicated that PAHs-d and PPAHs were more readily partitioned into water and SPM during normal and dry periods, respectively. The concentrations of PAHs-d saw significant changes in their spatial distribution, which rose in water and reduced in SPM in downstream of the Three Gorges Dam. This is due to the dam's blocking effect on sediment transport. Positive matrix factorization source analysis revealed biomass combustion upstream and vehicle emissions downstream as primary sources, shaped by the evolving energy consumption patterns of urban areas situated around the Yangtze River. The annual fluxes of PAHs-d in water and SPM of the Yangtze River were 90.40 t·yr[-1] and 11.95 t·yr[-1], representing 88.3 % and 11.7 % of the overall PAHs-d fluxes, respectively. The total fluxes of PAHs-d and PPAHs in water and SPM tended to increase spatially along the river, with growth rates exceeding 76 and 24 times, respectively. Interception within the Three Gorges Reservoir area has resulted in the differences in the concentration and transport distribution of PAHs-d and PPAHs upstream and downstream, which play important roles in reducing PAHs-d and PPAHs entry into the sea. Future studies on PAHs-d in Yangtze River basin tributaries and estuaries are essential.}, }
@article {pmid39643871, year = {2024}, author = {Zhang, W and Jin, Z and Huang, R and Huang, W and Li, L and He, Y and Zhou, J and Tian, C and Xiao, L and Li, P and Quan, M and Zhang, D and Du, Q}, title = {Multi-omics analysis reveals genetic architecture and local adaptation of coumarins metabolites in Populus.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1170}, pmid = {39643871}, issn = {1471-2229}, support = {No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 2021ZD0008//Major Science and Technology project of Inner Mongolia Autonomous Region/ ; No. 6212021//Project of the Natural Science Foundation of Beijing Municipality/ ; QNTD202305//Fundamental Research Funds for Central Universities of the Central South University/ ; }, mesh = {*Populus/genetics/metabolism ; *Coumarins/metabolism ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Adaptation, Physiological/genetics ; Gene Expression Regulation, Plant ; Genes, Plant ; Multiomics ; }, abstract = {BACKGROUND: Accumulation of coumarins plays key roles in response to immune and abiotic stress in plants, but the genetic adaptation basis of controlling coumarins in perennial woody plants remain unclear.
RESULTS: We detected 792 SNPs within 334 genes that were significantly associated with the phenotypic variations of 15 single-metabolic traits and multiple comprehensive index, such as principal components (PCs) of coumarins metabolites. Expression quantitative trait locus mapping uncovered that 337 eQTLs associated with the expression levels of 132 associated genes. Selective sweep revealed 55 candidate genes have potential selective signature among three geographical populations, highlighting that the coumarins biosynthesis have been encountered forceful local adaptation. Furthermore, we constructed a genetic network of seven candidate genes that coordinately regulate coumarins biosynthesis, revealing the multiple regulatory patterns affecting coumarins accumulation in Populus tomentosa. Validation of candidate gene variations in a drought-tolerated population and DUF538 heterologous transformation experiments verified the function of candidate genes and their roles in adapting to the different geographical conditions in poplar.
CONCLUSIONS: Our study uncovered the genetic regulation of the coumarins metabolic biosynthesis of Populus, and offered potential clues for drought-tolerance evaluation and regional improvement in woody plants.}, }
@article {pmid39642727, year = {2024}, author = {Mendrik, F and Hackney, CR and Cumming, VM and Waller, C and Hak, D and Dorrell, R and Hung, NN and Parsons, DR}, title = {The transport and vertical distribution of microplastics in the Mekong River, SE Asia.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136762}, doi = {10.1016/j.jhazmat.2024.136762}, pmid = {39642727}, issn = {1873-3336}, abstract = {Rivers are primary vectors of plastic debris to oceans, but sources, transport mechanisms, and fate of fluvial microplastics (<5 mm) remain poorly understood, impeding accurate predictions of microplastic flux, ecological risk and socio-economic impacts. We report on microplastic concentrations, characteristics and dynamics in the Mekong River, one of the world's largest and polluting rivers, in Cambodia and Vietnam. Sampling throughout the water column at multiple localities detected an average of 24 microplastics m[-3] (0.073 mg l[-1]). Concentrations increased downstream from rural Kampi, Cambodia (344 km from river mouth; 2 microplastics m[-3,] 0.006 mg l[-1]), to Can Tho, Vietnam (83 km from river mouth; 64 microplastics m[-3], 0.182 mg l[-1]) with most microplastics being fibres (53 %), followed by fragments (44 %) and the most common polymer being polyethylene terephthalate (PET) or polyester. Pathways of microplastic pollution are expected to be from urban wastewater highlighting the need for improved wastewater treatment in this region. On average, 86 % of microplastics are transported within the water column and consequently we identified an optimum sampling depth capturing a representative flux value, highlighting that sampling only the water surface substantially biases microplastic concentration predictions. Additionally, microplastic abundance does not linearly follow discharge changes during annual monsoonal floods or mirror siliciclastic sediment transport, as microplastic concentrations decrease rapidly during higher monsoon flows. The findings reveal complex microplastic transport in large rivers and call for improved sampling methods and predictive models to better assess environmental risk and guide policy.}, }
@article {pmid39642364, year = {2024}, author = {Lee, TY and Chen, CH and Chen, IM and Chen, HC and Liu, CM and Wu, SI and Hsiao, CK and Kuo, PH}, title = {Dynamic Bidirectional Associations Between Global Positioning System Mobility and Ecological Momentary Assessment of Mood Symptoms in Mood Disorders: Prospective Cohort Study.}, journal = {Journal of medical Internet research}, volume = {26}, number = {}, pages = {e55635}, pmid = {39642364}, issn = {1438-8871}, mesh = {Humans ; *Geographic Information Systems ; *Ecological Momentary Assessment ; Prospective Studies ; Male ; Adult ; Female ; Middle Aged ; *Mood Disorders/psychology ; Smartphone/statistics & numerical data ; Affect ; Mobile Applications ; }, abstract = {BACKGROUND: Although significant research has explored the digital phenotype in mood disorders, the time-lagged and bidirectional relationship between mood and global positioning system (GPS) mobility remains relatively unexplored. Leveraging the widespread use of smartphones, we examined correlations between mood and behavioral changes, which could inform future scalable interventions and personalized mental health monitoring.
OBJECTIVE: This study aims to investigate the bidirectional time lag relationships between passive GPS data and active ecological momentary assessment (EMA) data collected via smartphone app technology.
METHODS: Between March 2020 and May 2022, we recruited 45 participants (mean age 42.3 years, SD 12.1 years) who were followed up for 6 months: 35 individuals diagnosed with mood disorders referred by psychiatrists and 10 healthy control participants. This resulted in a total of 5248 person-days of data. Over 6 months, we collected 2 types of smartphone data: passive data on movement patterns with nearly 100,000 GPS data points per individual and active data through EMA capturing daily mood levels, including fatigue, irritability, depressed, and manic mood. Our study is limited to Android users due to operating system constraints.
RESULTS: Our findings revealed a significant negative correlation between normalized entropy (r=-0.353; P=.04) and weekly depressed mood as well as between location variance (r=-0.364; P=.03) and depressed mood. In participants with mood disorders, we observed bidirectional time-lagged associations. Specifically, changes in homestay were positively associated with fatigue (β=0.256; P=.03), depressed mood (β=0.235; P=.01), and irritability (β=0.149; P=.03). A decrease in location variance was significantly associated with higher depressed mood the following day (β=-0.015; P=.009). Conversely, an increase in depressed mood was significantly associated with reduced location variance the next day (β=-0.869; P<.001). These findings suggest a dynamic interplay between mood symptoms and mobility patterns.
CONCLUSIONS: This study demonstrates the potential of utilizing active EMA data to assess mood levels and passive GPS data to analyze mobility behaviors, with implications for managing disease progression in patients. Monitoring location variance and homestay can provide valuable insights into this process. The daily use of smartphones has proven to be a convenient method for monitoring patients' conditions. Interventions should prioritize promoting physical movement while discouraging prolonged periods of staying at home.}, }
@article {pmid39642189, year = {2024}, author = {Graham, AL and Regoes, RR}, title = {Dose-dependent interaction of parasites with tiers of host defense predicts "wormholes" that prolong infection at intermediate inoculum sizes.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012652}, pmid = {39642189}, issn = {1553-7358}, mesh = {*Host-Parasite Interactions/immunology ; Animals ; Computational Biology ; Parasites/physiology/immunology ; Immunity, Innate ; Models, Biological ; }, abstract = {Immune responses are induced by parasite exposure and can in turn reduce parasite burden. Despite such apparently simple rules of engagement, key drivers of within-host dynamics, including dose-dependence of defense and infection duration, have proven difficult to predict. Here, we model how varied inoculating doses interact with multi-tiered host defenses at a site of inoculation, by confronting barrier, innate, and adaptive tiers with replicating and non-replicating parasites across multiple orders of magnitude of dose. We find that, in general, intermediate parasite doses generate infections of longest duration because they are sufficient in number to breach barrier defenses, but insufficient to strongly induce subsequent tiers of defense. These doses reveal "wormholes" in defense from which parasites might profit: Deviation from the hypothesis of independent action, which postulates that each parasite has an independent probability of establishing infection, may therefore be widespread. Interestingly, our model predicts local maxima of duration at two doses-one for each tier transition. While some empirical evidence is consistent with nonlinear dose-dependencies, testing the predicted dynamics will require finer-scale dose variation than experiments usually incorporate. Our results help explain varied infection establishment and duration among differentially-exposed hosts and elucidate evolutionary pressures that shape both virulence and defense.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, pmid = {39642168}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Humans ; *Microbiota/physiology ; *Algorithms ; *Gastrointestinal Microbiome/physiology ; Microbial Interactions/physiology ; }, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39638881, year = {2024}, author = {Vojteková, J and Janizadeh, S and Vojtek, M and Tirpáková, A and Ruttkay, M and Petrovič, F}, title = {Prediction of potential occurrence of historical objects with defensive function in Slovakia using machine learning approach.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30350}, pmid = {39638881}, issn = {2045-2322}, support = {033UKF-4/2023//Kultúrna a Edukacná Grantová Agentúra MŠVVaŠ SR/ ; }, abstract = {In this article, we aim at the prediction of possible locations of already defunct historical objects with a defensive function (HODFs) in Slovakia, which have not been found and documented so far, using three machine learning methods. Specifically, we used the support vector machine, k-nearest neighbors, and random forest algorithms, which were trained based on the following five factors influencing the possible occurrence of HODFs: elevation, distance from a river, distance from a settlement, lithological rock type, and type of representative geoecosystems. Training and testing datasets were based on a database of already documented 605 HODFs, which were divided into 70% of training samples and 30% of testing samples. All of the three models reached the AUC-ROC value over 0.74 based on the testing dataset. The best performance was recorded by the random forest predictive model with the AUC-ROC value equal to 0.79. The results of the random forest model were also validated with the recently documented HODFs via the archeological research.}, }
@article {pmid39636475, year = {2024}, author = {Ganie, PA and Posti, R and Bharti, VS and Sehgal, VK and Sarma, D and Pandey, PK}, title = {Erosion landscape characterization in the Himalayan basin: insights from geospatial data and multi-criteria evaluation.}, journal = {Environmental monitoring and assessment}, volume = {197}, number = {1}, pages = {29}, pmid = {39636475}, issn = {1573-2959}, mesh = {India ; *Environmental Monitoring ; *Rivers/chemistry ; *Geographic Information Systems ; Soil Erosion ; Conservation of Natural Resources ; Hydrology ; }, abstract = {In regions characterized by mountainous landscapes, such as watersheds with high elevations, steep inclines, and rugged terrains, there exists an inherent susceptibility to water-induced soil erosion. This susceptibility underscores the importance of identifying areas prone to erosion to mitigate the loss of valuable natural resources and ensure their preservation over time. In response to this need, the current research employed a combination of four multi-criteria decision-making (MCDM) models, namely TOPSIS-AHP, VIKOR-AHP, ARAS-AHP, and CODAS-AHP, for the identification of areas susceptible to soil erosion within the Himalayan River basin of Nandakini, Uttarakhand, India. This identification was facilitated through the utilization of remote sensing and geospatial technologies. The study considered a total of 19 prioritization parameters that included morphological, topo-hydrological, climatic, and environmental factors specific to the Nandakini catchment for the purpose of prioritization modeling. The adoption of morphometric parameters in depicting the geological structures and hydrodynamic behavior of the river basin proves to be a crucial approach in locales where hydrological data may be scarce. The investigation delineated twenty watersheds within the catchment by employing SRTM DEM, SOI toposheets, and Geographic Information Systems (GIS), calculating the catchment's total area to be approximately 540.98 km[2]. The analysis determined that the catchment is classified as a 6th-order catchment, exhibiting mainly a sub-dendritic to dendritic drainage pattern. It was identified that the catchment is vulnerable to flooding and subsequent gully erosion due to the slow movement of surface runoff. Furthermore, the catchment's elongated shape and the compactness coefficient suggest a delayed peak runoff. The drainage texture ranged from very coarse to coarse, and the relief characteristics highlighted that the watersheds within the catchment possess a high relief ratio, thereby increasing their erosion vulnerability. Topo-hydrological indices revealed significant topographic variability and spatial differences in water availability and erosion potential across the basin. The efficacy of the MCDM models was evaluated through the Spearman's correlation coefficient test, alongside indices of intensity and percentage of change, to validate the findings. The ARAS-AHP and CODAS-AHP models were found to exhibit superior efficiency and higher accuracy relative to the other methods assessed. The insights gained from the ARAS-AHP and CODAS-AHP models are instrumental in the development of strategies for sustainable catchment management plans and inform decision-making processes regarding water resources management within the catchment.}, }
@article {pmid39635120, year = {2024}, author = {Qiu, Y and He, Z and Yu, X and Jia, G and Wang, Y}, title = {Analysis of factors influencing groundwater drought in the Loess zone of China.}, journal = {iScience}, volume = {27}, number = {10}, pages = {110929}, pmid = {39635120}, issn = {2589-0042}, abstract = {Understanding the characteristics and factors influencing groundwater resources is important for regional water resources management. The Gravity Recovery and Climate Experiment (GRACE)-based groundwater conditions were used to analyze the spatiotemporal characteristics of and the factors influencing groundwater storage (GWS) distribution in the Loess zone of the Yellow River Basin. The results revealed that the spatiotemporal distribution of GWS anomalies in the Loess zone of China was best explained by the first three components of the empirical orthogonal function (EOF), representing 85.6% of the total variance. The normalized difference vegetation index (NDVI) was significantly correlated with groundwater drought (p < 0.05). In addition, NDVI and evapotranspiration (ET) were the dominant factors influencing groundwater drought. NDVI was the dominant influencing factor in 67% and 80% of the total study area between 2002-2014 and 2015-2021, respectively. This study provides important guidance for a future ecological restoration plan in the Loess zone.}, }
@article {pmid39627996, year = {2024}, author = {Rodman, KC and Bradford, JB and Formanack, AM and Fulé, PZ and Huffman, DW and Kolb, TE and Miller-Ter Kuile, AT and Normandin, DP and Ogle, K and Pedersen, RJ and Schlaepfer, DR and Stoddard, MT and Waltz, AEM}, title = {Restoration treatments enhance tree growth and alter climatic constraints during extreme drought.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {}, number = {}, pages = {e3072}, doi = {10.1002/eap.3072}, pmid = {39627996}, issn = {1051-0761}, support = {22-DG-11030000-012//U.S. Forest Service/ ; }, abstract = {The frequency and severity of drought events are predicted to increase due to anthropogenic climate change, with cascading effects across forested ecosystems. Management activities such as forest thinning and prescribed burning, which are often intended to mitigate fire hazard and restore ecosystem processes, may also help promote tree resistance to drought. However, it is unclear whether these treatments remain effective during the most severe drought conditions or whether their impacts differ across environmental gradients. We used tree-ring data from a system of replicated, long-term (>20 years) experiments in the southwestern United States to evaluate the effects of forest restoration treatments (i.e., evidence-based thinning and burning) on annual growth rates (i.e., basal area increment; BAI) of ponderosa pine (Pinus ponderosa), a broadly distributed and heavily managed species in western North America. The study sites were established at the onset of the most extreme drought event in at least 1200 years and span much of the climatic niche of Rocky Mountain ponderosa pine. Across sites, tree-level BAI increased due to treatment, where trees in treated units grew 133.1% faster than trees in paired, untreated units. Likewise, trees in treated units grew an average of 85.6% faster than their pre-treatment baseline levels (1985 to ca. 2000), despite warm, dry conditions in the post-treatment period (ca. 2000-2018). Variation in the local competitive environment promoted variation in BAI, and larger trees were the fastest-growing individuals, irrespective of treatment. Tree thinning and prescribed fire altered the climatic constraints on growth, decreasing the effects of belowground moisture availability and increasing the effects of atmospheric evaporative demand over multi-year timescales. Our results illustrate that restoration treatments can enhance tree-level growth across sites spanning ponderosa pine's climatic niche, even during recent, extreme drought events. However, shifting climatic constraints, combined with predicted increases in evaporative demand in the southwestern United States, suggest that the beneficial effects of such treatments on tree growth may wane over the upcoming decades.}, }
@article {pmid39627652, year = {2024}, author = {Peltier, DMP and Carbone, MS and Ogle, K and Koch, GW and Richardson, AD}, title = {Decades-old carbon reserves are widespread among tree species, constrained only by sapwood longevity.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.20310}, pmid = {39627652}, issn = {1469-8137}, support = {149//Save the Redwoods League/ ; 1936205//Division of Integrative Organismal Systems/ ; 2053337//Division of Integrative Organismal Systems/ ; 1832218//Division of Environmental Biology/ ; 2213599//Division of Environmental Biology/ ; }, abstract = {Carbon reserves are distributed throughout plant cells allowing past photosynthesis to fuel current metabolism. In trees, comparing the radiocarbon (Δ[14]C) of reserves to the atmospheric bomb spike can trace reserve ages. We synthesized Δ[14]C observations of stem reserves in nine tree species, fitting a new process model of reserve building. We asked how the distribution, mixing, and turnover of reserves vary across trees and species. We also explored how stress (drought and aridity) and disturbance (fire and bark beetles) perturb reserves. Given sufficient sapwood, young (< 1 yr) and old (20-60+ yr) reserves were simultaneously present in single trees, including 'prebomb' reserves in two conifers. The process model suggested that most reserves are deeply mixed (30.2 ± 21.7 rings) and then respired (2.7 ± 3.5-yr turnover time). Disturbance strongly increased Δ[14]C mean ages of reserves (+15-35 yr), while drought and aridity effects on mixing and turnover were species-dependent. Fire recovery in Sequoia sempervirens also appears to involve previously unobserved outward mixing of old reserves. Deep mixing and rapid turnover indicate most photosynthate is rapidly metabolized. Yet ecological variation in reserve ages is enormous, perhaps driven by stress and disturbance. Across species, maximum reserve ages appear primarily constrained by sapwood longevity, and thus old reserves are probably widespread.}, }
@article {pmid39624726, year = {2024}, author = {Tian, T and Zhang, X and Zhang, F and Huang, X and Li, M and Quan, Z and Wang, W and Lei, J and Wang, Y and Liu, Y and Wang, JH}, title = {Harnessing AI for advancing pathogenic microbiology: a bibliometric and topic modeling approach.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1510139}, pmid = {39624726}, issn = {1664-302X}, abstract = {INTRODUCTION: The integration of artificial intelligence (AI) in pathogenic microbiology has accelerated research and innovation. This study aims to explore the evolution and trends of AI applications in this domain, providing insights into how AI is transforming research and practice in pathogenic microbiology.
METHODS: We employed bibliometric analysis and topic modeling to examine 27,420 publications from the Web of Science Core Collection, covering the period from 2010 to 2024. These methods enabled us to identify key trends, research areas, and the geographical distribution of research efforts.
RESULTS: Since 2016, there has been an exponential increase in AI-related publications, with significant contributions from China and the USA. Our analysis identified eight major AI application areas: pathogen detection, antibiotic resistance prediction, transmission modeling, genomic analysis, therapeutic optimization, ecological profiling, vaccine development, and data management systems. Notably, we found significant lexical overlaps between these areas, especially between drug resistance and vaccine development, suggesting an interconnected research landscape.
DISCUSSION: AI is increasingly moving from laboratory research to clinical applications, enhancing hospital operations and public health strategies. It plays a vital role in optimizing pathogen detection, improving diagnostic speed, treatment efficacy, and disease control, particularly through advancements in rapid antibiotic susceptibility testing and COVID-19 vaccine development. This study highlights the current status, progress, and challenges of AI in pathogenic microbiology, guiding future research directions, resource allocation, and policy-making.}, }
@article {pmid39622961, year = {2024}, author = {Jeong, D and Hyun, JY and Marchenkova, T and Matiukhina, D and Cho, S and Lee, J and Kim, DY and Li, Y and Darman, Y and Min, MS and Bardyuk, V and Lee, Y and Pandey, P and Lee, H}, title = {Genetic insights and conservation strategies for Amur tigers in Southwest Primorye Russia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29985}, pmid = {39622961}, issn = {2045-2322}, support = {550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 550-20190003//Ministry of Environment of the Republic of Korea, Convention on Biological Diversity under Bio-Bridge Initiative/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; 5260-20190100//Brain Korea-21 programme/ ; 5260-20200100//Brain Korea-21 programme/ ; A0449-2020010//Brain Korea-21 programme/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; Building Tumen River Corridor for Tigers and leopards: Genetic diversity of tigers and leopards using non-invasive technique 2022-2023//Tiger and Leopard Conservation Fund in Korea/ ; }, mesh = {Animals ; *Tigers/genetics ; *Conservation of Natural Resources ; *Genetic Variation ; *Microsatellite Repeats/genetics ; Male ; Female ; *DNA, Mitochondrial/genetics ; Russia ; Genetics, Population ; Population Density ; }, abstract = {Southwest Primorye hosts approximately 9% of the remaining wild Amur tiger population and represents hope for the revival of tigers in Northeast China and the Korean peninsula. Decades of conservation efforts have led to a significant increase in population size, from less than 10 individuals surviving in the region in 1996 to multiple folds today. However, while the population size has recovered since the mid-1900s, the effects of genetic depletion on evolutionary potential are not easily reversed. In this study, a non-invasive genetic analysis of the Amur tiger subpopulation in Southwest Primorye was conducted using microsatellite loci and mitochondrial genes to estimate genetic diversity, relatedness, and determine the impact of historical demographic dynamics. A total of 32 individuals (16 males, 15 females, and 1 unidentified sex) were identified, and signs of bottlenecks were detected, reflecting past demographic events. Low genetic variation observed in mitochondrial DNA also revealed genetic depletion within the population. Most individuals were found to be closely related to each other, raising concerns about inbreeding given the small population size and somewhat isolated environment from the main population in Sikhote-Alin. These findings emphasize the urgent need to establish ecological corridors to neighboring areas to restore genetic diversity and ensure the conservation of the Amur tiger population in Southwest Primorye.}, }
@article {pmid39622813, year = {2024}, author = {Monadjem, A and Montauban, C and Webala, PW and Laverty, TM and Bakwo-Fils, EM and Torrent, L and Tanshi, I and Kane, A and Rutrough, AL and Waldien, DL and Taylor, PJ}, title = {African bat database: curated data of occurrences, distributions and conservation metrics for sub-Saharan bats.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1309}, pmid = {39622813}, issn = {2052-4463}, mesh = {*Chiroptera/classification/physiology ; Animals ; Africa South of the Sahara ; *Conservation of Natural Resources ; *Databases, Factual ; Ecosystem ; Animal Distribution ; }, abstract = {Accurate knowledge of species distributions is foundational for effective conservation efforts. Bats are a diverse group of mammals, with important roles in ecosystem functioning. However, our understanding of bats and their ecological importance is hindered by poorly defined ranges, mostly as a result of under-recording. This issue is exacerbated in Africa by the ongoing rapid discovery of new species, both de novo and splits of existing species, and by inaccessibility to museum specimens that are mostly hosted outside of the continent. Here we present the African bat database - a curated set of 17,285 unique locality records of all 266 species of bats from sub-Saharan Africa, vouched for by specimens and/or genetic sequencing, and aligned with current taxonomy. Based on these records, we also present Maxent-based distribution models and calculate the IUCN Red List metrics for Extent of Occurrence and Area of Occupancy. This database and online visualization tool provide an important open-source resource and is expected to significantly advance studies in ecology, and aid in bat conservation.}, }
@article {pmid39622351, year = {2024}, author = {Nishimura, H and Nawa, N and Ogawa, T and Fushimi, K and Schwartz, BS and Fujiwara, T}, title = {Projections of future heat-related emergency hospitalizations for asthma under climate and demographic change scenarios: A Japanese nationwide time-series analysis.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120498}, doi = {10.1016/j.envres.2024.120498}, pmid = {39622351}, issn = {1096-0953}, abstract = {BACKGROUND: There is growing concern about climate impacts on human health. However, empirical evidence is lacking regarding future projections of heat-related asthma hospitalizations. This study aimed to project excess emergency hospitalizations for heat-related asthma exacerbation in Japan.
METHODS: Using Japanese nationwide administrative data from 2011 to 2019, we conducted an ecological time-series quasi-Poisson regression analysis to estimate the heat-related relative risk of emergency hospitalization for asthma over a lag of 0-3 days during the warm season (June to September). Heat exposure was defined as the region-specific daily mean temperature exceeding the locally defined minimum morbidity temperature percentile (MMP). Heat-related excess hospitalizations for asthma were projected under future climate and demographic change scenarios based on Shared Socioeconomic Pathways (SSPs).
RESULTS: We identified 75,829 emergency hospitalizations for asthma. The heat-related relative risk of hospitalization was 1.22 (95% confidence interval (CI): 1.12-1.33) at the 99th percentile temperature relative to the MMP, with the highest estimates for cases aged 0-14 years. Heat-related excess hospitalizations were projected to increase by 6.78 (95%CI: 5.84-7.67) times in 2091-2099 versus 2011-2019 along SSP5-8.5 when constant population structure was assumed. The increasing trend persisted even when the future population decline was considered (4.19 (95%CI: 3.53-4.85) times in 2091-2099 versus 2011-2019 under SSP5-8.5).
CONCLUSION: Future heat-related impacts on asthma exacerbation are expected to increase in Japan toward the end of this century, even when the future demographic change is considered. Our projections will contribute to resilient health systems adapting to ongoing climate change.}, }
@article {pmid39621910, year = {2024}, author = {Alfaro-Sánchez, R and Richardson, AD and Smith, SL and Johnstone, JF and Turetsky, MR and Cumming, SG and Le Moine, JM and Baltzer, JL}, title = {Permafrost instability negates the positive impact of warming temperatures on boreal radial growth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {50}, pages = {e2411721121}, pmid = {39621910}, issn = {1091-6490}, support = {15879//Aurora Research Institute (ARI)/ ; permafrost monitoring in the Mackenzie River Valley//Canadian Government | Natural Resources Canada (NRCan)/ ; MZ2021//María Zambrano program/ ; Small Research 2021 - SR21/1291//British Ecological Society (BES)/ ; Environmental Studies Research Fund and Cumulative Impacts Monitoring Program (Project 170)//Environment and Natural Resources, Northwest Territories (ENR, NWT)/ ; Discovery Grant support//Canadian Government | NSERC | RES'EAU-WaterNET/ ; Bonanza Creek LTER DEB-2224776//National Science Foundation (NSF)/ ; }, mesh = {*Permafrost ; *Trees/growth & development ; Temperature ; Taiga ; Global Warming ; Climate Change ; Forests ; }, abstract = {Climate warming can alleviate temperature and nutrient constraints on tree growth in boreal regions, potentially enhancing boreal productivity. However, in permafrost environments, warming also disrupts the physical foundation on which trees grow, leading to leaning trees or "drunken" forests. Tree leaning might reduce radial growth, undermining potential benefits of warming. Here, we found widespread radial growth reductions in southern latitude boreal forests since the 1980s. At mid latitudes, radial growth increased from ~1980 to ~2000 but showed recent signs of decline afterward. Increased growth was evident since the 1980 s at higher latitudes, where radial growth appears to be temperature limited. However, recent changes in permafrost stability, and the associated increased frequency of tree leaning events, emerged as a significant stressor, leading to reduced radial growth in boreal trees at the highest latitudes, where permafrost is extensive. We showed that trees growing in unstable permafrost sites allocated more nonstructural carbohydrate reserves to offset leaning which compromised radial growth and potential carbon uptake benefits of warming. This higher allocation of resources in drunken trees is needed to build the high-density reaction wood, rich in lignin, that is required to maintain a vertical position. With continued climate warming, we anticipate widespread reductions in radial growth in boreal forests, leading to lower carbon sequestration. These findings enhance our understanding of how climate warming and indirect effects, such as ground instability caused by warming permafrost, will affect boreal forest productivity in the future.}, }
@article {pmid39621775, year = {2024}, author = {Osiecka, AN and Bryndza, P and Briefer, EF and Wojczulanis-Jakubas, K}, title = {Long distance calls: Negligible information loss of little auk social vocalisations due to high frequency propagation losses.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1011961}, doi = {10.1371/journal.pcbi.1011961}, pmid = {39621775}, issn = {1553-7358}, mesh = {Animals ; *Vocalization, Animal/physiology ; Sound Spectrography/methods ; Computational Biology ; Acoustics ; Social Behavior ; }, abstract = {How well does the information contained in vocal signals travel through the environment? To assess the efficiency of information transfer in little auk (Alle alle, an Arctic seabird) calls over distance, we selected two of the social call types with the highest potential for individuality coding. Using available recordings of known individuals, we calculated the apparent source levels, with apparent maximum peak sound pressure level (ASPL) of 63 dB re 20 μPa at 1 m for both call types. Further, we created a sound attenuation model using meteorological data collected in the vicinity of the little auk colony in Hornsund, Spitsbergen. Using this model, we modelled the calls to reflect higher frequency filtering and sound level loss occurring during spherical spreading in perfect local conditions, down to the putative hearing threshold of the species, calculated to equal ASPL of signals "propagated" to roughly one kilometre. Those modelled calls were then used in a permuted discriminant function analysis, support vector machine models, and linear models of Beecher's information statistic, to investigate whether transmission loss will affect the retention of individual information of the signal. Calls could be correctly classified to individuals above chance level independently of the distance, down to and over the putative physiological hearing threshold. Interestingly, the information capacity of the signal did not decrease with its filtering and attenuation. While this study touches on signal properties purely and cannot provide evidence of the actual use by the animals, it shows that little auk signals can theoretically travel long distances with negligible information loss, and supports the hypothesis that vocalisations could facilitate long-distance communication in the species.}, }
@article {pmid39618809, year = {2024}, author = {Boyes, D and Young, MR and , and , and , and , and , and , and , }, title = {The genome sequence of the Straw Grass-veneer moth, Agriphila straminella (Denis & Schiffermüller), 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {433}, pmid = {39618809}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Straw Grass-veneer moth, Agriphila straminella (Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence has a length of 511.50 megabases. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,087 protein-coding genes.}, }
@article {pmid39616400, year = {2024}, author = {Asaaga, FA and Shakeer, I and Sriram, A and Chhotaria, K and Dutta, S and Narayanaswamy, D and Amankwaa, G and Chanda, MM and Hoti, SL and Young, JC and Purse, BV}, title = {Ties that bind: understanding One Health networks and participation for zoonoses prevention and control in India.}, journal = {One health outlook}, volume = {6}, number = {1}, pages = {24}, pmid = {39616400}, issn = {2524-4655}, abstract = {BACKGROUND: Cross-sectoral collaborations as exemplified by the One Health approach, are widely endorsed as pragmatic avenues for addressing zoonotic diseases, but operationalisation remain limited in low-and-middle income countries (LMICs). Complexities and competing interests and agendas of key stakeholders and the underlying politico-administrative context can all shape outcomes of collaborative arrangements. Evidence is building that organised collaborations are complex political initiatives where different objectives; individual and institutional agendas need to be reconciled to incentivise collaborations.
METHODS: Drawing on a qualitative network analysis of published sources on 'One Health' stakeholders supplemented with 26 multi-scale (national-state-district level) key-informant interviews (including policymakers, disease managers and public health experts), this paper characterises the fragmented and complex characteristics of institutional networks involved in zoonoses prevention and control in India.
RESULTS: Our results highlight how the local socio-political and institutional contexts interact to modulate how and when collaborations occur (or not), the associated contingencies and stakeholder innovations in circumventing existing barriers (e.g. competing interests, distrust between actors, departmental bureaucracy) to cross-sector collaborations and zoonoses management. Aside from principal actors negotiating common ground in some instance, they also capitalised on political/institutional pressure to subtly 'manipulate' their subordinates as a way of fostering collaboration, especially in instances when the institutional and political stakes are high.
CONCLUSION: Altogether our findings suggest that cross-sectoral collaborations are by-product of political and institutional tinkering as long as individual actors and institutional interests converge and these dynamics must be embraced to embed meaningful and sustainable collaborations in local socio-political and administrative contexts.}, }
@article {pmid39612036, year = {2024}, author = {Ma, D and Huang, Q and Wang, Q and Xu, H and Yan, Y}, title = {Detection of spatiotemporal changes in eco-environmental quality based on RSEI and SG filtering and its driving force analysis: a case study in Sichuan Province, China.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1274}, pmid = {39612036}, issn = {1573-2959}, support = {ZR2020MD025//Natural Science Foundation of Shandong Province/ ; 42171435//National Natural Science Foundation of China/ ; }, mesh = {China ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Forests ; Ecosystem ; Grassland ; Conservation of Natural Resources/methods ; }, abstract = {Landsat images were extracted using Google Earth Engine (GEE) platform and optimized by Savitzky-Golay (SG) filtering. The Remote Sensing Ecological Index (RSEI) method was used to analyze the eco-environmental quality in Sichuan Province in recent 20 years. In addition, Theil-Sen median method and Mann-Kendall (MK) test were used to test the change trend of eco-environmental quality. Furthermore, drivers were evaluated by partial correlation analysis, 2D scatter plots, and t tests. The results showed that (1) in the past 20 years, the eco-environmental quality of Sichuan Province was on the rise, and the eco-environmental quality in the western region was better than that in the eastern region. The eco-environmental quality was positively correlated with forest and grassland types, and negatively correlated with cultivated land and urban and rural construction land types. (2) The eco-environmental quality of Sichuan Province is linearly correlated with the digital elevation model, but poorly correlated with slope and slope direction. In the range of slope 0° ~ 9° and southeast direction, the eco-environmental quality is the worst. (3) The eco-environmental quality of Sichuan Province was most significantly affected by soil moisture and sunshine hours. The study can help us to understand and assess the health of ecosystems in Sichuan Province, provide a scientific basis for protecting and improving the environment, and guide the formulation and implementation of environmental protection policies.}, }
@article {pmid39609505, year = {2024}, author = {Alvarez-Mamani, E and Buettner, F and Beltran-Castanon, CA and Ibanez, AJ}, title = {Exploratory analysis of metabolic changes using mass spectrometry data and graph embeddings.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29570}, pmid = {39609505}, issn = {2045-2322}, support = {No. 174-2020-FONDECYT "Doctoral Programs in Peruvian Universities"//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica (CONCYTEC), and Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica (FONDECYT)/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; "The Max Planck Partner Group" (Max Planck Institute for Chemical Ecology-Jena)//Max-Planck-Gesellschaft/ ; Nº PE501086715-2024- PROCIENCIA)//CONCYTEC-Prociencia convocatoria E041-2024-01/ ; }, mesh = {*Metabolomics/methods ; *Mass Spectrometry/methods ; *Algorithms ; *Data Mining/methods ; Humans ; Deep Learning ; Metabolic Networks and Pathways ; Metabolome ; }, abstract = {Mass spectrometry (MS)-based metabolomics analysis is a powerful tool, but it comes with its own set of challenges. The MS workflow involves multiple steps before its interpretation in what is denominate data mining. Data mining consists of a two-step process. First, the MS data is ordered, arranged, and presented for filtering before being analyzed. Second, the filtered and reduced data are analyzed using statistics to remove further variability. This holds true particularly for MS-based untargeted metabolomics studies, which focused on understanding fold changes in metabolic networks. Since the task of filtering and identifying changes from a large dataset is challenging, automated techniques for mining untargeted MS-based metabolomic data are needed. The traditional statistics-based approach tends to overfilter raw data, which may result in the removal of relevant data and lead to the identification of fewer metabolomic changes. This limitation of the traditional approach underscores the need for a new method. In this work, we present a novel deep learning approach using node embeddings (powered by GNNs), edge embeddings, and anomaly detection algorithm to analyze the data generated by mass spectrometry (MS)-based metabolomics called GEMNA (Graph Embedding-based Metabolomics Network Analysis), for example for an untargeted volatile study on Mentos candy, the data clusters produced by GEMNA were better than the ones used traditional tools, i.e., GEMNA has [Formula: see text], vs. the traditional approach has [Formula: see text].}, }
@article {pmid39606930, year = {2024}, author = {Whyte, M and Wambui, KM and Musenge, E}, title = {Nigeria's malaria prevalence in 2015: a geospatial, exploratory district-level approach.}, journal = {Geospatial health}, volume = {19}, number = {2}, pages = {}, doi = {10.4081/gh.2024.1243}, pmid = {39606930}, issn = {1970-7096}, mesh = {Humans ; Nigeria/epidemiology ; *Malaria/epidemiology ; Prevalence ; Child, Preschool ; Infant ; *Spatial Analysis ; Female ; Male ; *Geographic Information Systems ; Socioeconomic Factors ; Adult ; Adolescent ; Child ; Middle Aged ; Young Adult ; }, abstract = {This study used data from the second Nigeria Malaria Indicator Survey (NMIS) conducted in 2015 to investigate the spatial distribution of malaria prevalence in the country and identify its associated factors. Nigeria is divided into 36 states with 109 senatorial districts, most of which are affected by malaria, a major cause of morbidity and mortality in children under five years of age. We carried out an ecological study with analysis at the senatorial district level. A malaria prevalence map was produced combining geographic information systems data from the Nigeria Malaria Indicator Survey (NMIS) of 2015 with shape files from an open data-sharing platform. Spatial autoregressive models were fitted using a set of key covariates. Malaria prevalence in children under-five was highest in Kebbi South senatorial district (70.6%). It was found that poorest wealth index (β = 0.10 (95% CI: 0.01, 0.20), p = 0.04), mothers having only secondary level of education (β = 0.78 (95% CI: 0.05, 1.51), p = 0.04) and households without mosquito bed nets (β = 0.21 (95% CI: 0.02, 0.39), p = 0.03) were all significantly associated with higher malaria prevalence. Moran's I (54.81, p<0.001) showed spatial dependence of malaria prevalence across contiguous districts and spatial autoregressive modelling demonstrated significant spill-over effect of malaria prevalence. Maps produced in this study provide a useful graphical representation of the spatial distribution of malaria prevalence based on NMIS-2015 data. Clustering of malaria prevalence in certain areas further highlights the need for sustained malaria elimination interventions across affected regions in order to break the chain of transmission.}, }
@article {pmid39602490, year = {2024}, author = {Soares, R and Azevedo, L and Vasconcelos, V and Pratas, D and Sousa, SF and Carneiro, J}, title = {Machine Learning-Driven Discovery and Database of Cyanobacteria Bioactive Compounds: A Resource for Therapeutics and Bioremediation.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {24}, pages = {9576-9593}, doi = {10.1021/acs.jcim.4c00995}, pmid = {39602490}, issn = {1549-960X}, mesh = {*Cyanobacteria/metabolism ; *Machine Learning ; *Biodegradation, Environmental ; *Drug Discovery ; Molecular Docking Simulation ; Databases, Factual ; Databases, Chemical ; Humans ; Software ; }, abstract = {Cyanobacteria strains have the potential to produce bioactive compounds that can be used in therapeutics and bioremediation. Therefore, compiling all information about these compounds to consider their value as bioresources for industrial and research applications is essential. In this study, a searchable, updated, curated, and downloadable database of cyanobacteria bioactive compounds was designed, along with a machine-learning model to predict the compounds' targets of newly discovered molecules. A Python programming protocol obtained 3431 cyanobacteria bioactive compounds, 373 unique protein targets, and 3027 molecular descriptors. PaDEL-descriptor, Mordred, and Drugtax software were used to calculate the chemical descriptors for each bioactive compound database record. The biochemical descriptors were then used to determine the most promising protein targets for human therapeutic approaches and environmental bioremediation using the best machine learning (ML) model. The creation of our database, coupled with the integration of computational docking protocols, represents an innovative approach to understanding the potential of cyanobacteria bioactive compounds. This resource, adhering to the findability, accessibility, interoperability, and reuse of digital assets (FAIR) principles, is an excellent tool for pharmaceutical and bioremediation researchers. Moreover, its capacity to facilitate the exploration of specific compounds' interactions with environmental pollutants is a significant advancement, aligning with the increasing reliance on data science and machine learning to address environmental challenges. This study is a notable step forward in leveraging cyanobacteria for both therapeutic and ecological sustainability.}, }
@article {pmid39600916, year = {2021}, author = {Boyes, D and Crowley, LM and , and , and , and , and , and , }, title = {The genome sequence of the harlequin ladybird, Harmonia axyridis (Pallas, 1773).}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {300}, pmid = {39600916}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Harmonia axyridis (the harlequin ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 426 megabases in span. The majority (99.98%) of the assembly is scaffolded into 8 chromosomal pseudomolecules, with the X sex chromosome assembled.}, }
@article {pmid39599286, year = {2024}, author = {Toghan, A and Alduaij, OK and Sanad, MMS and Elessawy, NA}, title = {Scalable Engineering of 3D Printing Filaments Derived from Recycling of Plastic Drinking Water Bottle and Glass Waste.}, journal = {Polymers}, volume = {16}, number = {22}, pages = {}, pmid = {39599286}, issn = {2073-4360}, support = {IMSIU-RG23086//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University/ ; }, abstract = {The most significant challenge that the world is currently facing is the development of beneficial industrial applications for solid waste. A novel strategy was implemented to produce a composite with varying loadings of glass waste nanoparticles (GWNP) in 5, 10, and 15 wt.% with recycled polyethylene terephthalate drinking water bottle waste (RPET). This strategy was based on glass and drinking water bottle waste. An analysis was conducted to evaluate the performance of the composite as filaments for 3D printer applications. This study evaluated the effect of GWNP addition on the chemical structure, thermal and mechanical characteristics of the composite. The Fourier Transform Infrared (FTIR) spectra of the filament composites and RPET composites exhibited similarities. However, the mechanical strength and thermal stability of the filament composites were enhanced due to the increased GWNP content. Furthermore, the results indicated that the filament developed could be utilized for 3D printing, as demonstrated by the successful fabrication of the filament composite, including 5 wt.% GWNP, using a 3D printer pen. The production of filaments using GWNP and RPET matrix presents a cost-effective, high-yield, and ecologically beneficial alternative. The present study may pave the way for the future advancement and utilization of 3D printing filaments by treating hazardous waste and using more ecologically friendly materials in design applications.}, }
@article {pmid39597377, year = {2024}, author = {Maślanka, P and Korycki, R}, title = {Material, Aerodynamic, and Operational Aspects of Single-Skin Paraglider.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {22}, pages = {}, pmid = {39597377}, issn = {1996-1944}, abstract = {The operating comfort of a paraglider is created by the aerodynamic parameters as well as the mass and packing volume of the wing. A classic paraglider has upper and lower covers. To reduce the material and manufacturing costs as well as protect the environment, it is possible to introduce a single-skin wing. This article conducts an analysis of a single-skin paraglider covered only with upper panels, whereas the lower cover is applied only at the leading and trailing edges. The analysis is theoretically oriented; aerodynamic and structural calculations were performed using the ANSYS environment. The single-skin structure was evaluated in terms of the predicted behavior during flight and the material's deformation under the influence of a specified pressure and the overloads acting on it. The results show that developing these structures may influence the creation of models with comparable aerodynamic characteristics to traditional ones. Additionally, the reduced masses and packing volumes of difficult-to-degrade materials are strongly correlated with saving costs and an ecological approach. No corresponding studies were found in the available literature. Thus, this presented analysis may result in a greater understanding and application of this paraglider type.}, }
@article {pmid39596552, year = {2024}, author = {Signore, IA and Donoso, G and Bocchieri, P and Tobar-Calfucoy, EA and Yáñez, CE and Carvajal-Silva, L and Silva, AX and Otth, C and Cappelli, C and Valenzuela Jorquera, H and Zapata-Contreras, D and Espinosa-Parrilla, Y and Zúñiga-Pacheco, P and Fuentes-Guajardo, M and Monardes-Ramírez, VA and Kochifas Velasquez, P and Muñoz, CA and Dorador, C and García-Araya, J and Campillay-Véliz, CP and Echeverria, C and Santander, RA and Cerpa, LC and Martínez, MF and Quiñones, LA and Lamoza Galleguillos, ER and Saez Hidalgo, J and Nova-Lamperti, E and Sanhueza, S and Giacaman, A and Acosta-Jamett, G and Verdugo, C and Plaza, A and Verdugo, C and Selman, C and Verdugo, RA and Colombo, A}, title = {The Chilean COVID-19 Genomics Network Biorepository: A Resource for Multi-Omics Studies of COVID-19 and Long COVID in a Latin American Population.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, pmid = {39596552}, issn = {2073-4425}, support = {ANID COVID0961, ANID COVID0789, ANID COVID1005, ANID COVID0585, ACT210085, FONDECYT 1170446, FONDECYT 1211480//Agencia Nacional de Investigación y Desarrollo/ ; MAG1995//Ministry of Education/ ; RED21193//Interuniversity Center for Healthy Aging/ ; VRID220.085.041-INI//University of Concepción/ ; }, mesh = {Humans ; *COVID-19/genetics/virology/epidemiology ; Chile ; *Biological Specimen Banks ; *Genomics/methods ; *SARS-CoV-2/genetics ; Male ; Female ; Adult ; Middle Aged ; Aged ; Latin America ; Multiomics ; }, abstract = {Although a lack of diversity in genetic studies is an acknowledged obstacle for personalized medicine and precision public health, Latin American populations remain particularly understudied despite their heterogeneity and mixed ancestry. This gap extends to COVID-19 despite its variability in susceptibility and clinical course, where ethnic background appears to influence disease severity, with non-Europeans facing higher hospitalization rates. In addition, access to high-quality samples and data is a critical issue for personalized and precision medicine, and it has become clear that the solution lies in biobanks. The creation of the Chilean COVID-19 Biorepository reported here addresses these gaps, representing the first nationwide multicentric Chilean initiative. It operates under rigorous biobanking standards and serves as one of South America's largest COVID cohorts. A centralized harmonization strategy was chosen and included unified standard operating procedures, a sampling coding system, and biobanking staff training. Adults with confirmed SARS-CoV-2 infection provided broad informed consent. Samples were collected to preserve blood, plasma, buffy coat, and DNA. Quality controls included adherence to the standard preanalytical code, incident reporting, and DNA concentration and absorbance ratio 260/280 assessments. Detailed sociodemographic, health, medication, and preexisting condition data were gathered. In five months, 2262 participants were enrolled, pseudonymized, and sorted by disease severity. The average Amerindian ancestry considering all participant was 44.0% [SD 15.5%], and this value increased to 61.2% [SD 19.5%] among those who self-identified as Native South Americans. Notably, 279 participants self-identified with one of 12 ethnic groups. High compliance (>90%) in all assessed quality controls was achieved. Looking ahead, our team founded the COVID-19 Genomics Network (C19-GenoNet) focused on identifying genetic factors influencing SARS-CoV-2 outcomes. In conclusion, this bottom-up collaborative effort aims to promote the integration of Latin American populations into global genetic research and welcomes collaborations supporting this endeavor. Interested parties are invited to explore collaboration opportunities through our catalog, accessible online.}, }
@article {pmid39595758, year = {2024}, author = {Aras, SG and Runyon, JR and Kazman, JB and Thayer, JF and Sternberg, EM and Deuster, PA}, title = {Is Greener Better? Quantifying the Impact of a Nature Walk on Stress Reduction Using HRV and Saliva Cortisol Biomarkers.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {11}, pages = {}, pmid = {39595758}, issn = {1660-4601}, support = {XX//The Institute for Integrative Health and Nature Sacred/ ; }, mesh = {Humans ; *Hydrocortisone/analysis/metabolism ; *Saliva/chemistry ; *Walking/physiology ; *Heart Rate/physiology ; Male ; Adult ; Female ; *Biomarkers/analysis/metabolism ; Stress, Psychological/metabolism/physiopathology ; Affect/physiology ; Stress, Physiological/physiology ; Young Adult ; Nature ; Middle Aged ; }, abstract = {The physiological impact of walking in nature was quantified via continuous heart rate variability (HRV), pre- and post-walk saliva cortisol measures, and self-reported mood and mindfulness scores for N = 17 participants who walked "The Green Road" at Walter Reed National Military Medical Center in Bethesda, Maryland. For N = 15 of the participants, HRV analysis revealed two main groups: group one individuals had a 104% increase (mean) in the root mean square standard deviation (RMSSD) and a 47% increase (mean) in the standard deviation of NN values (SDNN), indicating an overall reduction in physiological stress from walking the Green Road, and group two individuals had a decrease (mean) of 42% and 31% in these respective HRV metrics, signaling an increase in physiological stresses. Post-walk self-reported scores for vigor and mood disturbance were more robust for the Green Road than for a comparable urban road corridor and showed that a higher HRV during the walk was associated with improved overall mood. Saliva cortisol was lower after taking a walk for all participants, and it showed that walking the Green Road elicited a significantly larger reduction in cortisol of 53%, on average, when compared with 37% of walking along an urban road. It was also observed that the order in which individuals walked the Green Road and urban road also impacted their cortisol responses, with those walking the urban road before the Green Road showing a substantial reduction in cortisol, suggesting a possible attenuation effect of walking the Green Road first. These findings provide quantitative data demonstrating the stress-reducing effects of being in nature, thus supporting the health benefit value of providing access to nature more broadly in many settings.}, }
@article {pmid39594004, year = {2024}, author = {Alrhmoun, M and Sulaiman, N and Haq, SM and Abidullah, S and Prakofjewa, J and Krigas, N and Pieroni, A and Sõukand, R}, title = {Is Boiling Bitter Greens a Legacy of Ancient Crete? Contemporary Foraging in the Minoan Refugium of the Lasithi Plateau.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, pmid = {39594004}, issn = {2304-8158}, support = {N/A//University of Gastronomic Sciences, Pollenzo, Italy/ ; N/A//Department of Environmental Sciences, Informatics, and Statistics, Ca' Foscari Uni-versity of Venice, Italy/ ; }, abstract = {Wild greens (WGs) play a significant role in Mediterranean diets (MDs), reflecting botanical and cultural diversities, mainly influenced by a complex conglomerate of local human ecologies. This study investigates local ecological knowledge (LEK) linked to traditional gathering and consumption of WGs in the Lasithi Plateau of eastern Crete, where human genetic studies one decade ago showed very peculiar patterns, hypothesising that the Minoan civilisation took refuge there before it disappeared. A field ethnobotanical study was conducted to document the diversity of WGs and their detailed local culinary uses in the Lasithi area by interviewing 31 study participants. Fifty-nine folk taxa (species and subspecies) were recorded, corresponding to fifty-eight botanical taxa. A quotation index was measured to assess the cultural significance of WGs in the study areas; logistic regression analysis was adopted to understand the impact of sensory classifications of WGs and their local cooking methods. Lasithi's foraging showed a notable prevalence of bitter-tasting WGs, which play a central role in local cognition and culinary practices. This bitterness aspect of WGs, potentially influenced by cultural preferences and genetic factors, probably suggests a connection to the ancient Lasithi's inhabitants, i.e., Minoan dietary habits. We found that bitterness is the predominant sensory attribute in Lasithi, characterising 45.76% of the WGs. These findings underscore the complex interplay between local ecologies and biodiversity, LEK, and dietary traditions, highlighting the importance of WGs in understanding the evolution of foraging and plant culinary diversities across the Mediterranean.}, }
@article {pmid39592922, year = {2024}, author = {Das, VA and Gautam, B and Yadav, PK and Varadwaj, PK and Wadhwa, G and Singh, S}, title = {Computational approach to identify novel genomic features conferring high fitness in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 associated with plant growth promotion (PGP) in apple.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {1127}, pmid = {39592922}, issn = {1471-2229}, mesh = {*Bacillus/genetics/physiology ; *Malus/microbiology/genetics ; *Genome, Bacterial ; Genetic Fitness ; Genomics/methods ; Genomic Islands ; Computational Biology/methods ; }, abstract = {A comparative genomic analysis approach provides valuable information about genetic variations and evolutionary relationships among microorganisms, aiding not only in the identification of functional genes responsible for traits such as pathogenicity, antibiotic resistance, and metabolic capabilities but also in enhancing our understanding of microbial genomic diversity and their ecological roles, such as supporting plant growth promotion, thereby enabling the development of sustainable strategies for agriculture. We used two strains from different Bacillus species, Bacillus velezensis AK-0 and Bacillus atrophaeus CNY01, which have previously been reported to have PGP activity in apple, and performed comparative genomic analysis to understand their evolutionary process and obtain a mechanistic understanding of their plant growth-promoting activity. We identified genomic features such as mobile genetic elements (MGEs) that encode key proteins involved in the survival, adaptation and growth of these bacterial strains. The presence of genomic islands and intact prophage DNA in Bacillus atrophaeus CNY01 and Bacillus velezensis AK-0 suggests that horizontal gene transfer has contributed to their diversification and acquisition of adaptive traits, enhancing their evolutionary advantage. We also identified novel DNA motifs that are associated with key physiological processes and metabolic pathways.}, }
@article {pmid39591252, year = {2024}, author = {Baradaran, M and Salabi, F and Mahdavinia, M and Mohammadi, E and Vazirianzadeh, B and Avella, I and Kazemi, SM and Lüddecke, T}, title = {ScorpDb: A Novel Open-Access Database for Integrative Scorpion Toxinology.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591252}, issn = {2072-6651}, mesh = {*Scorpion Venoms/chemistry ; *Scorpions ; Animals ; Humans ; Databases, Factual ; Scorpion Stings/drug therapy ; Databases, Protein ; }, abstract = {Scorpion stings are a significant public health concern globally, particularly in tropical and subtropical regions. Scorpion venoms contain a diverse array of bioactive peptides, and different scorpion species around the world typically exhibit varying venom profiles, resulting in a wide range of envenomation symptoms. Despite their harmful effects, scorpion venom peptides hold immense potential for drug development due to their unique characteristics. Therefore, the establishment of a comprehensive database that catalogs scorpions along with their known venom peptides and proteins is imperative in furthering research efforts in this research area. We hereby present ScorpDb, a novel database that offers convenient access to data related to different scorpion species, the peptides and proteins found in their venoms, and the symptoms they can cause. To this end, the ScorpDb database has been primarily advanced to accommodate data on the Iranian scorpion fauna. From there, we propose future community efforts to include a larger diversity of scorpions and scorpion venom components. ScorpDb holds the promise to become a valuable resource for different professionals from a variety of research fields, like toxinologists, arachnologists, and pharmacologists. The database is available at https://www.scorpdb.com/.}, }
@article {pmid39591213, year = {2024}, author = {Roman-Ramos, H and Ho, PL}, title = {Current Technologies in Snake Venom Analysis and Applications.}, journal = {Toxins}, volume = {16}, number = {11}, pages = {}, pmid = {39591213}, issn = {2072-6651}, support = {2017/18398-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 309741/2023-8//National Council for Scientific and Technological Development/ ; }, mesh = {*Snake Venoms/chemistry ; Animals ; *Proteomics ; Humans ; Genomics ; Computational Biology ; Snakes ; }, abstract = {This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom function and its therapeutic potential. Despite significant progress, challenges such as the functional characterization of toxins and the development of cost-effective antivenoms remain. This review also discusses the future directions of venom research, emphasizing the need for interdisciplinary collaborations and new technologies (mRNAs, cryo-electron microscopy for structural determinations of toxin complexes, synthetic biology, and other technologies) to fully harness the biomedical potential of venoms and toxins from snakes and other animals.}, }
@article {pmid39589804, year = {2024}, author = {Arias, M and Behrendt, L and Dreßler, L and Raka, A and Perrier, C and Elias, M and Gomez, D and Renoult, JP and Tedore, C}, title = {Testing the equivalency of human "predators" and deep neural networks in the detection of cryptic moths.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voae146}, pmid = {39589804}, issn = {1420-9101}, abstract = {Researchers have shown growing interest in using deep neural networks (DNNs) to efficiently test the effects of perceptual processes on the evolution of color patterns and morphologies. Whether this is a valid approach remains unclear, as it is unknown whether the relative detectability of ecologically relevant stimuli to DNNs actually matches that of biological neural networks. To test this, we compare image classification performance by humans and six DNNs (AlexNet, VGG-16, VGG-19, ResNet-18, SqueezeNet, and GoogLeNet) trained to detect artificial moths on tree trunks. Moths varied in their degree of crypsis, conferred by different sizes and spatial configurations of transparent wing elements. Like humans, four of six DNN architectures found moths with larger transparent elements harder to detect. However, humans and only one DNN architecture (GoogLeNet) found moths with transparent elements touching one side of the moth's outline harder to detect than moths with untouched outlines. When moths were small, the camouflaging effect of transparent elements touching the moth's outline was reduced for DNNs but enhanced for humans. Prey size can thus interact with camouflage type in opposing directions in humans and DNNs, which warrants a deeper investigation of size interactions with a broader range of stimuli. Overall, our results suggest that humans and DNNs responses had some similarities, but not enough to justify the widespread use of DNNs for studies of camouflage.}, }
@article {pmid39586965, year = {2024}, author = {Gianicolo, E and Russo, A and Di Staso, R and Ronckers, CM and Schmidtmann, I and Wollschläger, D and Blettner, M}, title = {A municipality-specific analysis to investigate persistent increased incidence rates of childhood leukaemia near the nuclear power plant of Krümmel in Germany.}, journal = {European journal of epidemiology}, volume = {39}, number = {12}, pages = {1373-1378}, pmid = {39586965}, issn = {1573-7284}, mesh = {Humans ; Germany/epidemiology ; Child ; *Nuclear Power Plants ; Incidence ; Male ; Child, Preschool ; Female ; *Leukemia/epidemiology ; Adolescent ; Infant ; *Registries ; Leukemia, Radiation-Induced/epidemiology ; Infant, Newborn ; Cities/epidemiology ; Environmental Exposure/adverse effects/statistics & numerical data ; Risk Factors ; }, abstract = {Increased incidence rates for childhood leukaemia have been reported in municipalities close to the nuclear power plant (NPP) Krümmel (Geesthacht, Germany). Methodological challenges arise when analysing this association at ecological level. They include the use of an appropriate reference population, unstable estimates of standardised incidence ratios (SIRs), and the potential role of prevailing winds. The aim of our study is to address these challenges. The German Childhood Cancer Registry provided data on leukaemia in children under 15 years (2004-2019). The German Federal Statistical Office provided the population data. The study region included all municipalities with ≥ 75% surface area within 50 kms from the Krümmel NPP. We calculated SIRs using national and regional reference rates. Smoothed incidence relative rates (IRRs) were calculated and mapped to check for potential patterns associated with prevailing winds. Overall 356 cases of childhood leukaemia were observed in the study region (321 municipalities) during 2004-2019. SIRs based on national reference rates show nearly no difference to those calculated using the regional rates as reference. Increased SIR and IRR were observed in Geesthacht (observed-cases = eight; SIR = 2.29; 95% confidence interval: 0.99-4.51. IRR = 1.80; 95% credibility interval: 0.88-2.79). The analysis of the IRR map does not show patterns associated with prevailing winds. Using a regional population as the reference, we found evidence that there may still be an increased risk for childhood leukaemia in Geesthacht. However, IRR estimates are uncertain and credibility intervals are compatible with the absence of elevated risk. The persistent evidence of risk of childhood leukaemia in Geesthacht warrants further epidemiological surveillance.}, }
@article {pmid39585857, year = {2024}, author = {Adderley-Heron, K and Chow-Fraser, P}, title = {Unsupervised classification of Blanding's turtle (Emydoidea blandingii) behavioural states from multi-sensor biologger data.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0314291}, pmid = {39585857}, issn = {1932-6203}, mesh = {Animals ; *Turtles/physiology/classification ; Female ; Male ; *Behavior, Animal/physiology ; Accelerometry ; Markov Chains ; Geographic Information Systems ; Nesting Behavior/physiology ; }, abstract = {Classifying animal behaviors in their natural environments is both challenging and ecologically important, but the use of biologgers with multiple sensors has significantly advanced this research beyond the capabilities of traditional methods alone. Here, we show how biologgers containing an integrated tri-axial accelerometer, GPS logger and immersion sensor were used to infer behavioural states of a cryptic, freshwater turtle, the Blanding's turtle (Emydoidea blandingii). Biologgers were attached to three males and five females that reside in two undisturbed coastal marshes in northeastern Georgian Bay (Ontario, Canada) between May and July 2023. Raw acceleration values were separated into static and dynamic acceleration and subsequently used to calculate overall dynamic body acceleration (ODBA) and pitch. The unsupervised Hidden Markov Model (HMM) successfully differentiated five behavioural states as follows: active in water, resting in water, active out of water, resting in water, and nesting. Overall accuracy of the classification was 93.8%, and except for nesting (79%), all other behaviours were above 92%. There were significant differences in daily activity budgets between male and female turtles, with females spending a greater proportion of time active out of water, and inactive out of the water, while males spent a greater proportion of time active in water. These differences were likely a result of large seasonal life-history requirements such as nesting and mate finding. Accurate classification of behavioural states is important for researchers to understand fine-scale activities carried out during the active season and how environmental variables may influence the behaviours of turtles in their natural habitats.}, }
@article {pmid39585479, year = {2024}, author = {Sahak, AS and Karsli, F and Saraj, MA}, title = {Evaluating the impact of urban sprawl on the urban ecological status using GIS and remote sensing from 2000 to 2021: a case study of Herat City, Afghanistan.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1246}, pmid = {39585479}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; *Urbanization ; *Cities ; Afghanistan ; Conservation of Natural Resources/methods ; Ecosystem ; }, abstract = {Urbanization often incurs environmental costs, as fertile agricultural and forested lands are converted into urban areas. Herat City is currently undergoing significant urban transformation. This research aims to assess the impact of urban sprawl on Herat City's urban ecological status during 2000, 2013, and 2021, using GIS and remote sensing. The urban expansion intensity index was used to measure urban sprawl. The Mean Remote Sensing Ecological Index (MRSEI), integrating known granulation entropy (KGE) and comprehensive distance-based ranking (COBRA) algorithms, was utilized to evaluate urban ecological status. The random forest (RF) supervised machine learning-based algorithm was used to classify the study area into four categories (Built-up, Bare-land, Water, and Vegetation). Findings indicate rapid development from 2000 to 2013, followed by moderate expansion until 2021. Urban ecological quality degradation is observed in various directions over time, with the southeast consistently demonstrating excellent status. Interestingly, while good and excellent urban ecological status decreases over two decades, poor and very poor conditions improve. The research underscores an inverse relationship between urban expansion intensity and ecological status, highlighting the need for improved strategies to mitigate environmental decline. These findings will inform Afghan governmental bodies and international organizations, enabling them to better address resource consumption, ecological disruptions, social inequalities, and foster sustainable development.}, }
@article {pmid39583330, year = {2024}, author = {Hakkenberg, CR and Clark, ML and Bailey, T and Burns, P and Goetz, SJ}, title = {Ladder fuels rather than canopy volumes consistently predict wildfire severity even in extreme topographic-weather conditions.}, journal = {Communications earth & environment}, volume = {5}, number = {1}, pages = {721}, pmid = {39583330}, issn = {2662-4435}, abstract = {Drivers of forest wildfire severity include fuels, topography and weather. However, because only fuels can be actively managed, quantifying their effects on severity has become an urgent research priority. Here we employed GEDI spaceborne lidar to consistently assess how pre-fire forest fuel structure affected wildfire severity across 42 California wildfires between 2019-2021. Using a spatial-hierarchical modeling framework, we found a positive concave-down relationship between GEDI-derived fuel structure and wildfire severity, marked by increasing severity with greater fuel loads until a decline in severity in the tallest and most voluminous forest canopies. Critically, indicators of canopy fuel volumes (like biomass and height) became decoupled from severity patterns in extreme topographic and weather conditions (slopes >20°; winds > 9.3 m/s). On the other hand, vertical continuity metrics like layering and ladder fuels more consistently predicted severity in extreme conditions - especially ladder fuels, where sparse understories were uniformly associated with lower severity levels. These results confirm that GEDI-derived fuel estimates can overcome limitations of optical imagery and airborne lidar for quantifying the interactive drivers of wildfire severity. Furthermore, these findings have direct implications for designing treatment interventions that target ladder fuels versus entire canopies and for delineating wildfire risk across topographic and weather conditions.}, }
@article {pmid39581005, year = {2024}, author = {Tinsley, E and Froidevaux, JSP and Jones, G}, title = {The location of solar farms within England's ecological landscape: Implications for biodiversity conservation.}, journal = {Journal of environmental management}, volume = {372}, number = {}, pages = {123372}, doi = {10.1016/j.jenvman.2024.123372}, pmid = {39581005}, issn = {1095-8630}, mesh = {*Biodiversity ; England ; *Conservation of Natural Resources ; *Ecosystem ; Solar Energy ; Farms ; Geographic Information Systems ; Ecology ; Agriculture ; }, abstract = {A global energy transition to using sustainable renewable sources is being driven by global agreements. Simultaneously there is a call for increased biodiversity conservation. This creates a green-green dilemma, where the expansion of renewables could lead to the demise of biodiversity if not carefully assessed, managed and monitored. Recognition of the dilemma is central to the development of Sustainable Development Goals. It is therefore important to understand whether renewable energy sources such as solar farms are being sited in areas where they have minimal impact on biodiversity. If solar farms were sited with minimal impacts on biodiversity, we hypothesised that they would be less likely to be sited close to ecologically sensitive areas than near random points. We used Geographic Information System methods to explore the density of solar photovoltaic (PV) farms in England and assessed their siting relative to sensitive ecological features, including priority habitat types, designated sites, and land conservation initiatives. We compared the area of 25 sensitive ecological features around solar farms and random points across three spatial scales (100 m, 1000 m, and 6000 m radius scales). Solar farms were distributed throughout England, with the highest concentration in South West England. Solar sites were primarily surrounded by habitats with anthropogenic influences, such as agricultural and urban settings. Priority habitats, such as woodland, grassland, wetland and heathland, were more extensive around random points across spatial scales (except for woodland at the largest scale). Most designated sites were significantly more extensive around random points. We conclude that, under current planning regulations, solar sites in England are being placed appropriately with regard to sensitive ecological habitats, and are often sited in areas already impacted by farming and development. Adaptive planning should be implemented to ensure that the evolving research around biodiversity and solar farms is incorporated into decision making, and monitoring is completed across the lifespan of solar farms to assess impacts and effective mitigation.}, }
@article {pmid39580513, year = {2024}, author = {Li, J and Weckwerth, W and Waldherr, S}, title = {Network structure and fluctuation data improve inference of metabolic interaction strengths with the inverse Jacobian.}, journal = {NPJ systems biology and applications}, volume = {10}, number = {1}, pages = {137}, pmid = {39580513}, issn = {2056-7189}, support = {201806010428//China Scholarship Council (CSC)/ ; }, mesh = {Humans ; *Algorithms ; *Metabolic Networks and Pathways/genetics ; *Breast Neoplasms/metabolism/genetics ; *Metabolomics/methods ; Cell Line, Tumor ; Models, Biological ; Computational Biology/methods ; Female ; Systems Biology/methods ; }, abstract = {Based on high-throughput metabolomics data, the recently introduced inverse differential Jacobian algorithm can infer regulatory factors and molecular causality within metabolic networks close to steady-state. However, these studies assumed perturbations acting independently on each metabolite, corresponding to metabolic system fluctuations. In contrast, emerging evidence puts forward internal network fluctuations, particularly from gene expression fluctuations, leading to correlated perturbations on metabolites. Here, we propose a novel approach that exploits these correlations to quantify relevant metabolic interactions. By integrating enzyme-related fluctuations in the construction of an appropriate fluctuation matrix, we are able to exploit the underlying reaction network structure for the inverse Jacobian algorithm. We applied this approach to a model-based artificial dataset for validation, and to an experimental breast cancer dataset with two different cell lines. By highlighting metabolic interactions with significantly changed interaction strengths, the inverse Jacobian approach identified critical dynamic regulation points which are confirming previous breast cancer studies.}, }
@article {pmid39578727, year = {2024}, author = {Ang'ang'o, LM and Herren, JK and Tastan Bishop, Ö}, title = {Bioinformatics analysis of the Microsporidia sp. MB genome: a malaria transmission-blocking symbiont of the Anopheles arabiensis mosquito.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1132}, pmid = {39578727}, issn = {1471-2164}, mesh = {*Anopheles/microbiology/parasitology/genetics ; Animals ; *Microsporidia/genetics ; *Symbiosis ; *Computational Biology/methods ; *Genome, Fungal ; Malaria/transmission ; Phylogeny ; Mosquito Vectors/microbiology/genetics ; Genomics/methods ; RNA Interference ; }, abstract = {BACKGROUND: The use of microsporidia as a disease-transmission-blocking tool has garnered significant attention. Microsporidia sp. MB, known for its ability to block malaria development in mosquitoes, is an optimal candidate for supplementing malaria vector control methods. This symbiont, found in Anopheles mosquitoes, can be transmitted both vertically and horizontally with minimal effects on its mosquito host. Its genome, recently sequenced from An. arabiensis, comprises a compact 5.9 Mbp.
RESULTS: Here, we analyze the Microsporidia sp. MB genome, highlighting its major genomic features, gene content, and protein function. The genome contains 2247 genes, predominantly encoding enzymes. Unlike other members of the Enterocytozoonida group, Microsporidia sp. MB has retained most of the genes in the glycolytic pathway. Genes involved in RNA interference (RNAi) were also identified, suggesting a mechanism for host immune suppression. Importantly, meiosis-related genes (MRG) were detected, indicating potential for sexual reproduction in this organism. Comparative analyses revealed similarities with its closest relative, Vittaforma corneae, despite key differences in host interactions.
CONCLUSION: This study provides an in-depth analysis of the newly sequenced Microsporidia sp. MB genome, uncovering its unique adaptations for intracellular parasitism, including retention of essential metabolic pathways and RNAi machinery. The identification of MRGs suggests the possibility of sexual reproduction, offering insights into the symbiont's evolutionary strategies. Establishing a reference genome for Microsporidia sp. MB sets the foundation for future studies on its role in malaria transmission dynamics and host-parasite interactions.}, }
@article {pmid39576832, year = {2024}, author = {Devadhasan, A and Kolodny, O and Carja, O}, title = {Competition for resources can reshape the evolutionary properties of spatial structure.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012542}, pmid = {39576832}, issn = {1553-7358}, support = {R35 GM147445/GM/NIGMS NIH HHS/United States ; T32 EB009403/EB/NIBIB NIH HHS/United States ; }, mesh = {*Ecosystem ; Humans ; *Biological Evolution ; Computational Biology ; Mutation ; Models, Biological ; Computer Simulation ; }, abstract = {Many evolving ecosystems have spatial structures that can be conceptualized as networks, with nodes representing individuals or homogeneous subpopulations and links the patterns of spread between them. Prior models of evolution on networks do not take ecological niche differences and eco-evolutionary interplay into account. Here, we combine a resource competition model with evolutionary graph theory to study how heterogeneous topological structure shapes evolutionary dynamics under global frequency-dependent ecological interactions. We find that the addition of ecological competition for resources can produce a reversal of roles between amplifier and suppressor networks for deleterious mutants entering the population. We show that this effect is a nonlinear function of ecological niche overlap and discuss intuition for the observed dynamics using simulations and analytical approximations. We use these theoretical results together with spatial representations from imaging data to show that, for ductal carcinoma, where tumor growth is highly spatially constrained, with cells confined to a tree-like network of ducts, the topological structure can lead to higher rates of deleterious mutant hitchhiking with metabolic driver mutations, compared to tumors characterized by different spatial topologies.}, }
@article {pmid39570994, year = {2024}, author = {Madden, WG and Jin, W and Lopman, B and Zufle, A and Dalziel, B and E Metcalf, CJ and Grenfell, BT and Lau, MSY}, title = {Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012616}, pmid = {39570994}, issn = {1553-7358}, mesh = {*Measles/epidemiology ; Humans ; *Neural Networks, Computer ; *Disease Outbreaks/statistics & numerical data ; *Endemic Diseases/statistics & numerical data ; England/epidemiology ; Wales/epidemiology ; Computational Biology ; Forecasting/methods ; Epidemiological Models ; }, abstract = {Measles is an important infectious disease system both for its burden on public health and as an opportunity for studying nonlinear spatio-temporal disease dynamics. Traditional mechanistic models often struggle to fully capture the complex nonlinear spatio-temporal dynamics inherent in measles outbreaks. In this paper, we first develop a high-dimensional feed-forward neural network model with spatial features (SFNN) to forecast endemic measles outbreaks and systematically compare its predictive power with that of a classical mechanistic model (TSIR). We illustrate the utility of our model using England and Wales measles data from 1944-1965. These data present multiple modeling challenges due to the interplay between metapopulations, seasonal trends, and nonlinear dynamics related to demographic changes. Our results show that while the TSIR model yields similarly performant short-term (1 to 2 biweeks ahead) forecasts for highly populous cities, our neural network model (SFNN) consistently achieves lower root mean squared error (RMSE) across other forecasting windows. Furthermore, we show that our spatial-feature neural network model, without imposing mechanistic assumptions a priori, can uncover gravity-model-like spatial hierarchy of measles spread in which major cities play an important role in driving regional outbreaks. We then turn our attention to integrative approaches that combine mechanistic and machine learning models. Specifically, we investigate how the TSIR can be utilized to improve a state-of-the-art approach known as Physics-Informed-Neural-Networks (PINN) which explicitly combines compartmental models and neural networks. Our results show that the TSIR can facilitate the reconstruction of latent susceptible dynamics, thereby enhancing both forecasts in terms of mean absolute error (MAE) and parameter inference of measles dynamics within the PINN. In summary, our results show that appropriately designed neural network-based models can outperform traditional mechanistic models for short to long-term forecasts, while simultaneously providing mechanistic interpretability. Our work also provides valuable insights into more effectively integrating machine learning models with mechanistic models to enhance public health responses to measles and similar infectious disease systems.}, }
@article {pmid39570888, year = {2024}, author = {Cuesta-Aguirre, DR and Malgosa, A and Santos, C}, title = {An easy-to-use pipeline to analyze amplicon-based Next Generation Sequencing results of human mitochondrial DNA from degraded samples.}, journal = {PloS one}, volume = {19}, number = {11}, pages = {e0311115}, pmid = {39570888}, issn = {1932-6203}, mesh = {*DNA, Mitochondrial/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Forensic Genetics/methods ; DNA, Ancient/analysis ; }, abstract = {Genome and transcriptome examinations have become more common due to Next-Generation Sequencing (NGS), which significantly increases throughput and depth coverage while reducing costs and time. Mitochondrial DNA (mtDNA) is often the marker of choice in degraded samples from archaeological and forensic contexts, as its higher number of copies can improve the success of the experiment. Among other sequencing strategies, amplicon-based NGS techniques are currently being used to obtain enough data to be analyzed. There are some pipelines designed for the analysis of ancient mtDNA samples and others for the analysis of amplicon data. However, these pipelines pose a challenge for non-expert users and cannot often address both ancient and forensic DNA particularities and amplicon-based sequencing simultaneously. To overcome these challenges, a user-friendly bioinformatic tool was developed to analyze the non-coding region of human mtDNA from degraded samples recovered in archaeological and forensic contexts. The tool can be easily modified to fit the specifications of other amplicon-based NGS experiments. A comparative analysis between two tools, MarkDuplicates from Picard and dedup parameter from fastp, both designed for duplicate removal was conducted. Additionally, various thresholds of PMDtools, a specialized tool designed for extracting reads affected by post-mortem damage, were used. Finally, the depth coverage of each amplicon was correlated with its level of damage. The results obtained indicated that, for removing duplicates, dedup is a better tool since retains more non-repeated reads, that are removed by MarkDuplicates. On the other hand, a PMDS = 1 in PMDtools was the threshold that allowed better differentiation between present-day and ancient samples, in terms of damage, without losing too many reads in the process. These two bioinformatic tools were added to a pipeline designed to obtain both haplotype and haplogroup of mtDNA. Furthermore, the pipeline presented in the present study generates information about the quality and possible contamination of the sample. This pipeline is designed to automatize mtDNA analysis, however, particularly for ancient samples, some manual analyses may be required to fully validate results since the amplicons that used to be more easily recovered were the ones that had fewer reads with damage, indicating that special care must be taken for poor recovered samples.}, }
@article {pmid39569566, year = {2024}, author = {Sung, ML and León, C and Reisman, JI and Gordon, KS and Kerns, RD and Li, W and Liu, W and Mitra, A and Yu, H and Becker, WC}, title = {Disparities in Receipt of Medications for Opioid Use Disorder Before and During the COVID-19 Pandemic in the US Veterans Health Administration.}, journal = {Substance use & addiction journal}, volume = {}, number = {}, pages = {29767342241293334}, doi = {10.1177/29767342241293334}, pmid = {39569566}, issn = {2976-7350}, abstract = {BACKGROUND: Populations disproportionately impacted by the opioid epidemic are less likely to receive medications for opioid use disorder (MOUD; OUD). The COVID-19 pandemic exacerbated these disparities. We performed an ecological survey of subpopulations to compare differences in MOUD receipt among Veterans with OUD before versus during the pandemic.
METHODS: Using 2 cross-sections of 2 time periods of national Veterans Health Administration electronic health record data, we calculated proportions of Veterans with any MOUD receipt by demographics, Elixhauser comorbidity index, and natural language processing (NLP)-derived substance use and social determinants of health in each time period. We evaluated differences in MOUD receipt before and during the pandemic by patient characteristics using Chi-square and Cohen's h for effect size.
RESULTS: Among 62 195 patients with OUD before the pandemic, the proportion prescribed MOUD increased from 46.5% before to 47.5% (P = .0003) during the pandemic. Statistically significant increased receipt of MOUD was observed for patients who were ≥55 years, men, White, with Elixhauser comorbidity indices of 2 and ≥5, and with NLP-derived indicators of substance use. There was a decrease that did not achieve statistical significance in MOUD receipt from before to during the pandemic for patients who were women, Black, Latinx, and food insecure.
CONCLUSIONS: The proportions of patients with OUD prescribed MOUD increased from before to during the pandemic. However, Veterans who were women, Black, Latinx, and food insecure did not experience these increases. These patients may benefit from interventions such as targeted outreach efforts to improve MOUD engagement to reduce OUD harms.}, }
@article {pmid39569448, year = {2024}, author = {Yu, Y and Edelson, M and Pham, A and Pekar, JE and Johnson, B and Post, K and Kuo, TT}, title = {Distributed, immutable, and transparent biomedical limited data set request management on multi-capacity network.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocae288}, pmid = {39569448}, issn = {1527-974X}, support = {R01EB031030//U.S. National Institutes of Health/ ; }, abstract = {OBJECTIVE: Our study aimed to expedite data sharing requests of Limited Data Sets (LDS) through the development of a streamlined platform that allows distributed, immutable management of network activities, provides transparent and intuitive auditing of data access history, and systematically evaluated it on a multi-capacity network setting for meaningful efficiency metrics.
MATERIALS AND METHODS: We developed a blockchain-based system with six types of smart contracts to automate the LDS sharing process among major stakeholders. Our workflow included metadata initialization, access-request processing, and audit-log querying. We evaluated our system using synthetic data on three machines with varying specifications to emulate real-world scenarios. The data employed included ∼1000 researcher requests and ∼360 000 log queries.
RESULTS: On average, it took ∼2.5 s to register and respond to a researcher access request. The average runtime for an audit-log query with non-empty output was ∼3 ms. The runtime metrics at each institution showed general trends affiliated with their computational capacity.
DISCUSSION: Our system can reduce the LDS sharing request time from potentially hours to seconds, while enhancing data access transparency in a multi-institutional setting. There were variations in performance across sites that could be attributed to differences in hardware specifications. The performance gains became marginal beyond certain hardware thresholds, pointing to the influence of external factors such as network speeds.
CONCLUSION: Our blockchain-based system can potentially accelerate clinical research by strengthening the data access process, expediting access and delivery of data links, increasing transparency with clear audit trails, and reinforcing trust in medical data management. Our smart contracts are available at: https://github.com/graceyufei/LDS-Request-Management.}, }
@article {pmid39568559, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Silver-barred Sober moth, Aproaerema taeniolella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {500}, pmid = {39568559}, issn = {2398-502X}, abstract = {We present a genome assembly of a female Silver-barred Sober moth Aproaerema taeniolella (Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a length of 636.60 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,274 protein-coding genes.}, }
@article {pmid39564491, year = {2024}, author = {Zhang, Y and Wang, M and Huang, M and Zhao, J}, title = {Innovative strategies and challenges mosquito-borne disease control amidst climate change.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1488106}, pmid = {39564491}, issn = {1664-302X}, abstract = {The revival of the transmission dynamics of mosquito-borne diseases grants striking challenges to public health intensified by climate change worldwide. This inclusive review article examines multidimensional strategies and challenges linked to climate change and the epidemiology of mosquito-borne diseases such as malaria, dengue, Zika, chikungunya, and yellow fever. It delves into how the biology, pathogenic dynamics, and vector distribution of mosquitoes are influenced by continuously rising temperatures, modified rainfall patterns, and extreme climatic conditions. We also highlighted the high likelihood of malaria in Africa, dengue in Southeast Asia, and blowout of Aedes in North America and Europe. Modern predictive tools and developments in surveillance, including molecular gears, Geographic Information Systems (GIS), and remote sensing have boosted our capacity to predict epidemics. Integrated data management techniques and models based on climatic conditions provide a valuable understanding of public health planning. Based on recent data and expert ideas, the objective of this review is to provide a thoughtful understanding of existing landscape and upcoming directions in the control of mosquito-borne diseases regarding changing climate. This review determines emerging challenges and innovative vector control strategies in the changing climatic conditions to ensure public health.}, }
@article {pmid39563951, year = {2024}, author = {Sivell, O and Hawkes, WLS and , and , and , and , and , and , and , }, title = {The genome sequence of the silvery leafcutter bee, Megachile leachella Curtis, 1828.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {415}, pmid = {39563951}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Megachile leachella (the silvery leafcutter bee; Arthropoda; Insecta; Hymenoptera; Megachilidae). The genome sequence is 573.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 21.04 kilobases in length.}, }
@article {pmid39563229, year = {2024}, author = {Toth, AL and Wyatt, CDR and Masonbrink, RE and Geist, KS and Fortune, R and Scott, SB and Favreau, E and Rehan, SM and Sumner, S and Gardiner, MM and Sivakoff, FS}, title = {New genomic resources inform transcriptomic responses to heavy metal toxins in the common Eastern bumble bee Bombus impatiens.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1106}, pmid = {39563229}, issn = {1471-2164}, support = {20176701326595//USDA National Institute of Food and Agriculture/ ; 1929239//NSF DEB-NERC/ ; }, mesh = {Animals ; Bees/genetics/drug effects ; *Metals, Heavy/toxicity ; *Transcriptome ; Genomics/methods ; Molecular Sequence Annotation ; Gene Expression Profiling ; Genome, Insect ; Toxins, Biological/genetics ; }, abstract = {BACKGROUND: The common Eastern bumble bee Bombus impatiens is native to North America and is the main commercially reared pollinator in the Americas. There has been extensive research on this species related to its social biology, applied pollination, and genetics. The genome of this species was previously sequenced using short-read technology, but recent technological advances provide an opportunity for substantial improvements. This species is common in agricultural and urban environments, and heavy metal contaminants produced by industrial processes can negatively impact it. To begin to identify possible mechanisms underlying responses to these toxins, we used RNA-sequencing to examine how exposure to a cocktail of four heavy metals at field-realistic levels from industrial areas affected B. impatiens worker gene expression.
RESULTS: PacBio long-read sequencing resulted in 544x coverage of the genome, and HiC technology was used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high quality, chromosome-level assembly. The sequenced genome size is 266.6 Mb and BRAKER3 annotation produced 13,938 annotated genes. The genome and annotation show high completeness, with ≥ 96% of conserved Eukaryota and Hymenoptera genes present in both the assembly and annotated genes. RNA sequencing of heavy metal exposed workers revealed 603 brain and 34 fat body differentially expressed genes. In the brain, differentially expressed genes had biological functions related to chaperone activity and protein folding.
CONCLUSIONS: Our data represent a large improvement in genomic resources for this important model species-with 10% more genome coverage than previously available, and a high-quality assembly into 18 chromosomes, the expected karyotype for this species. The new gene annotation added 777 new genes. Altered gene expression in response to heavy metal exposure suggests a possible mechanism for how these urban toxins are negatively impacting bee health, specifically by altering protein folding in the brain. Overall, these data are useful as a general high quality genomic resource for this species, and provide insight into mechanisms underlying tissue-specific toxicological responses of bumble bees to heavy metals.}, }
@article {pmid39561196, year = {2024}, author = {Konzen, E and Delahay, RJ and Hodgson, DJ and McDonald, RA and Brooks Pollock, E and Spencer, SEF and McKinley, TJ}, title = {Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012592}, pmid = {39561196}, issn = {1553-7358}, mesh = {Animals ; *Mustelidae/microbiology ; *Tuberculosis, Bovine/epidemiology/transmission/diagnosis ; Cattle ; *Animals, Wild/microbiology ; United Kingdom/epidemiology ; Models, Biological ; Mycobacterium bovis ; Computational Biology/methods ; Disease Reservoirs/microbiology/veterinary ; Ireland/epidemiology ; }, abstract = {Bovine tuberculosis (bTB) has significant socio-economic and welfare impacts on the cattle industry in parts of the world. In the United Kingdom and Ireland, disease control is complicated by the presence of infection in wildlife, principally the European badger. Control strategies tend to be applied to whole populations, but better identification of key sources of transmission, whether individuals or groups, could help inform more efficient approaches. Mechanistic transmission models can be used to better understand key epidemiological drivers of disease spread and identify high-risk individuals and groups if they can be adequately fitted to observed data. However, this is a significant challenge, especially within wildlife populations, because monitoring relies on imperfect diagnostic test information, and even under systematic surveillance efforts (such as capture-mark-recapture sampling) epidemiological events are only partially observed. To this end we develop a stochastic compartmental model of bTB transmission, and fit this to individual-level data from a unique > 40-year longitudinal study of 2,391 badgers using a recently developed individual forward filtering backward sampling algorithm. Modelling challenges are further compounded by spatio-temporal meta-population structures and age-dependent mortality. We develop a novel estimator for the individual effective reproduction number that provides quantitative evidence for the presence of superspreader badgers, despite the population-level effective reproduction number being less than one. We also infer measures of the hidden burden of infection in the host population through time; the relative likelihoods of competing routes of transmission; effective and realised infectious periods; and longitudinal measures of diagnostic test performance. This modelling framework provides an efficient and generalisable way to fit state-space models to individual-level data in wildlife populations, which allows identification of high-risk individuals and exploration of important epidemiological questions about bTB and other wildlife diseases.}, }
@article {pmid39556417, year = {2024}, author = {Helgeson, SA and Mudgalkar, RM and Jacobs, KA and Lee, AS and Sanghavi, D and Moreno Franco, P and Brooks, IS and , }, title = {Association Between X/Twitter and Prescribing Behavior During the COVID-19 Pandemic: Retrospective Ecological Study.}, journal = {JMIR infodemiology}, volume = {4}, number = {}, pages = {e56675}, pmid = {39556417}, issn = {2564-1891}, support = {U24 TR002306/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Retrospective Studies ; *Hydroxychloroquine/therapeutic use ; *Social Media ; United States/epidemiology ; *COVID-19/epidemiology ; *Practice Patterns, Physicians' ; Pandemics ; COVID-19 Drug Treatment ; Male ; Female ; Middle Aged ; SARS-CoV-2/drug effects ; }, abstract = {BACKGROUND: Social media has become a vital tool for health care providers to quickly share information. However, its lack of content curation and expertise poses risks of misinformation and premature dissemination of unvalidated data, potentially leading to widespread harmful effects due to the rapid and large-scale spread of incorrect information.
OBJECTIVE: We aim to determine whether social media had an undue association with the prescribing behavior of hydroxychloroquine, using the COVID-19 pandemic as the setting.
METHODS: In this retrospective study, we gathered the use of hydroxychloroquine in 48 hospitals in the United States between January and December 2020. Social media data from X/Twitter was collected using Brandwatch, a commercial aggregator with access to X/Twitter's data, and focused on mentions of "hydroxychloroquine" and "Plaquenil." Tweets were categorized by sentiment (positive, negative, or neutral) using Brandwatch's sentiment analysis tool, with results classified by date. Hydroxychloroquine prescription data from the National COVID Cohort Collaborative for 2020 was used. Granger causality and linear regression models were used to examine relationships between X/Twitter mentions and prescription trends, using optimum time lags determined via vector auto-regression.
RESULTS: A total of 581,748 patients with confirmed COVID-19 were identified. The median daily number of positive COVID-19 cases was 1318.5 (IQR 1005.75-1940.3). Before the first confirmed COVID-19 case, hydroxychloroquine was prescribed at a median rate of 559 (IQR 339.25-728.25) new prescriptions per day. A day-of-the-week effect was noted in both prescriptions and case counts. During the pandemic in 2020, hydroxychloroquine prescriptions increased significantly, with a median of 685.5 (IQR 459.75-897.25) per day, representing a 22.6% rise from baseline. The peak occurred on April 2, 2020, with 3411 prescriptions, a 397.6% increase. Hydroxychloroquine mentions on X/Twitter peaked at 254,770 per day on April 5, 2020, compared to a baseline of 9124 mentions per day before January 21, 2020. During this study's period, 3,823,595 total tweets were recorded, with 10.09% (n=386,115) positive, 37.87% (n=1,448,030) negative, and 52.03% (n=1,989,450) neutral sentiments. A 1-day lag was identified as the optimal time for causal association between tweets and hydroxychloroquine prescriptions. Univariate analysis showed significant associations across all sentiment types, with the largest impact from positive tweets. Multivariate analysis revealed only neutral and negative tweets significantly affected next-day prescription rates.
CONCLUSIONS: During the first year of the COVID-19 pandemic, there was a significant association between X/Twitter mentions and the number of prescriptions of hydroxychloroquine. This study showed that X/Twitter has an association with the prescribing behavior of hydroxychloroquine. Clinicians need to be vigilant about their potential unconscious exposure to social media as a source of medical knowledge, and health systems and organizations need to be more diligent in identifying expertise, source, and quality of evidence when shared on social media platforms.}, }
@article {pmid39555185, year = {2024}, author = {Yang, D and Hashizume, M and Tobías, A and Honda, Y and Roye, D and Oh, J and Dang, TN and Kim, Y and Abrutzky, R and Guo, Y and Tong, S and Coelho, MSZS and Saldiva, PHN and Lavigne, E and Correa, PM and Ortega, NV and Osorio, S and Kyselý, J and Urban, A and Orru, H and Indermitte, E and Jaakkola, J and Ryti, N and Pascal, M and Huber, V and Schneider, A and Katsouyanni, K and Analitis, A and Entezari, A and Mayvaneh, F and Goodman, P and Zeka, A and Michelozzi, P and de'Donato, F and Alahmad, B and Diaz, MH and la Cruz Valencia, C and Overcenco, A and Houthuijs, D and Ameling, C and Rao, S and Nunes, B and Madureira, J and Holo-Bâc, IH and Scovronick, N and Acquaotta, F and Kim, H and Lee, W and Íñiguez, C and Forsberg, B and Vicedo-Cabrera, AM and Ragettli, MS and Guo, YL and Pan, SC and Li, S and Sera, F and Zanobetti, A and Schwartz, J and Armstrong, B and Gasparrini, A and Chung, Y}, title = {Temporal change in minimum mortality temperature under changing climate: A multicountry multicommunity observational study spanning 1986-2015.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {8}, number = {5}, pages = {e334}, pmid = {39555185}, issn = {2474-7882}, support = {MR/R013349/1/MRC_/Medical Research Council/United Kingdom ; MR/V034162/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: The minimum mortality temperature (MMT) or MMT percentile (MMTP) is an indicator of population susceptibility to nonoptimum temperatures. MMT and MMTP change over time; however, the changing directions show region-wide heterogeneity. We examined the heterogeneity of temporal changes in MMT and MMTP across multiple communities and in multiple countries.
METHODS: Daily time-series data for mortality and ambient mean temperature for 699 communities in 34 countries spanning 1986-2015 were analyzed using a two-stage meta-analysis. First, a quasi-Poisson regression was employed to estimate MMT and MMTP for each community during the designated subperiods. Second, we pooled the community-specific temporally varying estimates using mixed-effects meta-regressions to examine temporal changes in MMT and MMTP in the entire study population, as well as by climate zone, geographical region, and country.
RESULTS: Temporal increases in MMT and MMTP from 19.5 °C (17.9, 21.1) to 20.3 °C (18.5, 22.0) and from the 74.5 (68.3, 80.6) to 75.0 (71.0, 78.9) percentiles in the entire population were found, respectively. Temporal change was significantly heterogeneous across geographical regions (P < 0.001). Temporal increases in MMT were observed in East Asia (linear slope [LS] = 0.91, P = 0.02) and South-East Asia (LS = 0.62, P = 0.05), whereas a temporal decrease in MMT was observed in South Europe (LS = -0.46, P = 0.05). MMTP decreased temporally in North Europe (LS = -3.45, P = 0.02) and South Europe (LS = -2.86, P = 0.05).
CONCLUSIONS: The temporal change in MMT or MMTP was largely heterogeneous. Population susceptibility in terms of optimum temperature may have changed under a warming climate, albeit with large region-dependent variations.}, }
@article {pmid39549265, year = {2024}, author = {Rayamajhi, N and Rivera-Colón, AG and Minhas, BF and Cheng, CC and Catchen, JM}, title = {The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/g3journal/jkae267}, pmid = {39549265}, issn = {2160-1836}, abstract = {The Antarctic bald notothen, Trematomus borchgrevinki (family Nototheniidae) occupies a high latitude, ice-laden environment and represents an extreme example of cold-specialization among fishes. We present the first, high quality, chromosome-scale genome of a female T. borchgrevinki individual comprised of 23 putative chromosomes, the largest of which is 65 megabasepairs (Mbp) in length. The total length of the genome 935.13 Mbp, composed of 2,094 scaffolds, with a scaffold N50 of 42.67 Mbp. Annotation yielded 22,192 protein coding genes while 54.75% of the genome was occupied by repetitive elements; an analysis of repeats demonstrated that an expansion occurred in recent time. Conserved synteny analysis revealed that the genome architecture of T. borchgrevinki is largely maintained with other members of the notothenioid clade, although several significant translocations and inversions are present, including the fusion of orthologous chromosomes 8 and 11 into a single element. This genome will serve as a cold-specialized model for comparisons to other members of the notothenioid adaptive radiation.}, }
@article {pmid39548719, year = {2024}, author = {Chen, Y and Gao, Y and Zhang, Z and Zhan, A}, title = {Multi-Omics Inform Invasion Risks Under Global Climate Change.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17588}, doi = {10.1111/gcb.17588}, pmid = {39548719}, issn = {1365-2486}, support = {2022GDASZH-2022010106//GDAS Special Project of Science and Technology Development/ ; 2024A1515010914//Guangdong Basic and Applied Basic Research Foundation/ ; 42106098//National Natural Science Foundation of China/ ; 32061143012//National Natural Science Foundation of China/ ; 42276126//National Natural Science Foundation of China/ ; 32371753//National Natural Science Foundation of China/ ; }, mesh = {*Climate Change ; *Introduced Species ; *Genomics ; Urochordata/genetics ; Epigenomics ; Adaptation, Physiological/genetics ; Animals ; Multiomics ; }, abstract = {Global climate change is exacerbating biological invasions; however, the roles of genomic and epigenomic variations and their interactions in future climate adaptation remain underexplored. Using the model invasive ascidian Botryllus schlosseri across the Northern Hemisphere, we investigated genomic and epigenomic responses to future climates and developed a framework to assess future invasion risks. We employed generalized dissimilarity modeling and gradient forest analyses to assess genomic and epigenomic offsets under climate change. Our results showed that populations with genomic maladaptation did not geographically overlap with those experiencing epigenomic maladaptation, suggesting that genomic and epigenomic variations play complementary roles in adaptation to future climate conditions. By integrating genomic and epigenomic offsets into the genome-epigenomic index, we predicted that populations with lower index values were less maladapted, indicating a higher risk of future invasions. Native populations exhibited lower offsets than invasive populations, suggesting greater adaptive potentials and higher invasion risks under future climate change scenarios. These results highlight the importance of incorporating multi-omics data into predictive models to study future climate (mal)adaptation and assess invasion risks under global climate change.}, }
@article {pmid39548060, year = {2024}, author = {Conrad, RE and Brink, CE and Viver, T and Rodriguez-R, LM and Aldeguer-Riquelme, B and Hatt, JK and Venter, SN and Rossello-Mora, R and Amann, R and Konstantinidis, KT}, title = {Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {9906}, pmid = {39548060}, issn = {2041-1723}, support = {1831582//NSF | BIO | Division of Environmental Biology (DEB)/ ; }, mesh = {*Homologous Recombination ; *Escherichia coli/genetics/classification ; Genome, Bacterial ; Microbiota/genetics ; Evolution, Molecular ; Gene Flow ; Phylogeny ; Computational Biology/methods ; }, abstract = {Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in both Salinibacter ruber, an environmental halophilic organism, and Escherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.}, }
@article {pmid39547957, year = {2024}, author = {Kwon, EJ and Lee, H and Shin, U and Kim, ES and Myung, K and Kim, J and Park, JH and Kim, K and Lee, Y and Oh, CK and Kim, YH}, title = {Ionizing radiation inhibits zebrafish embryo hatching through induction of tissue inhibitors of metalloproteinases (TIMPs) expression.}, journal = {The FEBS journal}, volume = {291}, number = {24}, pages = {5470-5485}, doi = {10.1111/febs.17318}, pmid = {39547957}, issn = {1742-4658}, support = {IBS-R022-D1//Institute for Basic Science/ ; RS-2023-00223591//National Research Foundation of Korea/ ; RS-2023-00301938//National Research Foundation of Korea/ ; RS-2024-00439078//National Research Foundation of Korea/ ; //KREONET/ ; }, mesh = {Animals ; *Zebrafish/genetics/embryology/metabolism ; *Radiation, Ionizing ; *Tissue Inhibitor of Metalloproteinases/metabolism/genetics ; *Gene Expression Regulation, Developmental/radiation effects ; *Embryo, Nonmammalian/radiation effects/metabolism ; Zebrafish Proteins/genetics/metabolism ; }, abstract = {Ionizing radiation (IR) has garnered growing attention because of its biological effects on aquatic organisms and humans. Here, we identify the most impacted organs and uncover the molecular mechanisms causing the changes in the context of vertebrate development using single-cell RNA sequencing. Alterations in cellular composition and biological functions were explored using transcriptomic profiling of zebrafish embryos exposed to 5 Gy. Single-cell RNA sequencing analyses unveiled notable shifts in the proportions of brain/central nervous system and hatching gland clusters. Although IR exposure led to increased expression of hatching enzymes, a significant but mild delay in hatching was observed following 5 Gy IR exposure. Gene Ontology analysis showed an increased expression of tissue inhibitors of metalloproteinases (TIMPs), known as matrix metalloproteinase inhibitors, which was confirmed via whole-mount in situ hybridization. Correlation analysis linked TIMPs to transcription factors cebpb and cebpd, which were significantly correlated post-IR exposure. Although no morphological changes were observed in some organs, including the brain, the study reveals substantial alterations in developing vertebrates. Notably, despite increased hatching enzymes, elevated TIMPs in the hatching gland suggest a regulatory mechanism impacting hatching activity. This research contributes to comprehending the ecological repercussions of IR exposure, emphasizing the importance of safety measures for aquatic ecosystems and overall environmental health.}, }
@article {pmid39546825, year = {2025}, author = {Meyer, A and Ndiaye, B and Larkins, A and Chaters, G and Gilbert, W and Huntington, B and Ilboudo, G and Dione, M and Jemberu, WT and Diouf, MN and Fall, AG and Fall, M and Lo, M and Rushton, J}, title = {Economic assessment of animal disease burden in Senegalese small ruminants.}, journal = {Preventive veterinary medicine}, volume = {234}, number = {}, pages = {106382}, doi = {10.1016/j.prevetmed.2024.106382}, pmid = {39546825}, issn = {1873-1716}, mesh = {Animals ; Senegal/epidemiology ; *Goat Diseases/economics/epidemiology ; *Goats ; Sheep ; *Sheep Diseases/economics/epidemiology ; Cost of Illness ; Animal Husbandry/economics/methods ; }, abstract = {Small ruminant production in sub-Saharan Africa is limited by a range of constraints, including animal health issues. This study aimed at estimating the impact of these issues on the small ruminant production in Senegal in a holistic manner, using an approach developed by the Global Burden of Animal Diseases (GBADs) programme. The estimation focused on the mixed crop-livestock system, representing a large proportion (>60 %) of the small ruminant population in the country. It was based on existing data collected via a systematic literature review, acquisition of secondary datasets from local stakeholders, and expert elicitation. A dynamic population model was used to calculate the gross margin of the sector under both the current health constraints and an ideal health state, where animals are not exposed to causes of morbidity and mortality. The difference between the current and ideal health scenarios, termed the Animal Health Loss Envelope (AHLE), provides a quantitative measure of the farm-level cost of disease in the system. The all-cause AHLE was estimated at 292 billion FCFA (468 million USD, with 95 % prediction interval 216 - 366 billion FCFA) per year for 2022, for a population of 8.8 million animals. The contribution of Peste des Petits Ruminants (PPR) was modelled separately, as an example of attributing part of the AHLE to a specific disease cause. PPR was estimated to contribute 5 % of the total AHLE. The animal disease burden experienced by Senegalese livestock keepers was largely due to loss in animals and production, with relatively small amounts of animal health expenditure. Implementation of this study contributed to the further development of the GBADs approach. Such estimates can support decision making at all levels, from investment decisions at the international level to local disease awareness campaigns targeting livestock keepers.}, }
@article {pmid39545367, year = {2024}, author = {Heuck, MK and Powell, JR and Kath, J and Birnbaum, C and Frew, A}, title = {Evaluating the Usefulness of the C-S-R Framework for Understanding AM Fungal Responses to Climate Change in Agroecosystems.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17566}, doi = {10.1111/gcb.17566}, pmid = {39545367}, issn = {1365-2486}, support = {DE220100479//Australian Research Council (ARC) Discovery Early Career Researcher Award (DECRA)/ ; FT190100590//Australian Research Council Future Fellowship/ ; }, mesh = {*Climate Change ; *Mycorrhizae/physiology ; *Agriculture ; *Ecosystem ; Symbiosis ; }, abstract = {Arbuscular mycorrhizal (AM) fungi play a key role in terrestrial ecosystems by forming symbiotic relationships with plants and may confer benefits for sustainable agriculture, by reducing reliance on harmful fertiliser and pesticide inputs and enhancing plant resilience against insect herbivores. Despite their ecological importance, critical gaps in understanding AM fungal ecology limit predictions of their responses to global change in agroecosystems. However, predicting climate change impacts on AM fungi is important for maintaining crop productivity and ecosystem stability. Efforts to classify AM fungi based on functional traits, such as the competitor, stress-tolerator, ruderal (C-S-R) framework, aim to address these gaps but face challenges due to the obligate symbiotic nature of the fungi. As the framework is still widely used, we evaluate its applicability in predicting global change impacts on AM fungal communities in agroecosystems. Chagnon's adaptation of the C-S-R framework for AM fungi aligns with some study outcomes (e.g., under the context of water limitation) but faces challenges when used in complex climate change scenarios, varying agricultural conditions and/or extreme climatic conditions. The reliance on a limited dataset to classify AM fungal families further limits accurate predictions of AM fungal community dynamics. Trait data collection could support a nuanced understanding of AM fungi and leveraging AM fungal databases could streamline data management and analysis, enhancing efforts to clarify AM fungal responses to environmental change and guide ecosystem management practices. Thus, while the C-S-R framework holds promise, it requires additional AM fungal trait data for validation and improvement of its predictive power. Conclusively, before designing experiments based on life-history strategies and developing new frameworks tailored to AM fungi a critical first step is to gain a comprehensive understanding of their traits.}, }
@article {pmid39543597, year = {2024}, author = {Rajovic, N and Grubor, N and Cirkovic, A and Maheswaran, R and Bath, PA and Green, D and Bellantuono, I and Milicevic, O and Kanazir, S and Miljus, D and Zivkovic, S and Vidojevic, D and Mickovski, N and Rakocevic, I and Ivanovic, I and Mladenovic, A and Goyder, E and Milic, N}, title = {Insights into relationship of environmental inequalities and multimorbidity: a population-based study.}, journal = {Environmental health : a global access science source}, volume = {23}, number = {1}, pages = {99}, pmid = {39543597}, issn = {1476-069X}, support = {200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200110/WT_/Wellcome Trust/United Kingdom ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200007//Ministry of Science, Innovation and Technological Development of the Republic of Serbia/ ; 200110/WT_/Wellcome Trust/United Kingdom ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; 164294//UKRI Global Challenges Research Fund/ ; }, mesh = {Humans ; Middle Aged ; *Multimorbidity ; Adult ; Male ; Female ; Serbia/epidemiology ; Aged ; Young Adult ; *Air Pollutants/analysis ; Adolescent ; Environmental Exposure/adverse effects ; Air Pollution/analysis/adverse effects ; Prevalence ; Water Quality ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Substantial inequalities in the overall prevalence and patterns of multimorbidity have been widely reported, but the causal mechanisms are complex and not well understood. This study aimed to identify common patterns of multimorbidity in Serbia and assess their relationship with air pollutant concentrations and water quality indicators.
METHODS: This ecological study was conducted on a nationally representative sample of the Serbian population. Data were obtained from the European Health Interview (EHIS) Survey, a periodic study designed to assess population health using widely recognized standardized instruments. The study included 13,069 participants aged 15 and older, randomly selected through a multistage stratified sampling design. Multimorbidity was defined as having two or more self-reported diagnoses of chronic non-communicable diseases. Latent class analysis (LCA) was performed to identify clusters of multimorbidity. Concentrations of particulate matter (PM10), sulfur dioxide (SO2), nitrogen dioxide (NO2), carbon monoxide (CO), and ozone (O3), as well as water quality indicators, were obtained from the Serbian Environmental Protection Agency.
RESULTS: The overall prevalence of multimorbidity was 33.4% [32.6%-34.2%]. Six latent classes of multimorbidity were identified: Healthy, Multicondition, Cardiovascular, Metabolic syndrome, Respiratory, and Musculoskeletal. Annual increases in PM10 and SO2 concentrations, as well as daily increases in O3 concentrations, significantly raised the odds of having multimorbidity (OR = 1.02, 95% CI 1.02-1.03; OR = 1.01, 95% CI 1.00-1.02 and OR = 1.03, 95% CI 1.02-1.03, respectively). A pattern of increased risk was observed with rising levels of water contamination. Exposure to physico-chemical, microbiological and combined contamination was associated with a 3.92%, 5.17% and 5.54% higher probability, respectively, of having multiple chronic conditions. There was strong evidence that air pollutants, as well as chemical and microbial water contamination, were significantly associated with higher odds of the most common clusters of multimorbidity identified by LCA.
CONCLUSION: There is compelling evidence of an association between multimorbidity and environmental pollution, suggesting that exposure to air pollutants and water contaminants may contribute to disease accumulation and help explain geographically and socioeconomically patterned inequalities. These findings underscore the need for extensive studies that simultaneously measure both multimorbidity and pollution to explore their complex interrelationships.}, }
@article {pmid39543483, year = {2024}, author = {Rzehak, T and Praeg, N and Galla, G and Seeber, J and Hauffe, HC and Illmer, P}, title = {Comparison of commonly used software pipelines for analyzing fungal metabarcoding data.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1085}, pmid = {39543483}, issn = {1471-2164}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *Software ; Animals ; Cattle ; Computational Biology/methods ; Feces/microbiology ; Soil Microbiology ; }, abstract = {BACKGROUND: Metabarcoding targeting the internal transcribed spacer (ITS) region is commonly used to characterize fungal communities of various environments. Given their size and complexity, raw ITS sequences are necessarily processed and quality-filtered with bioinformatic pipelines. However, such pipelines are not yet standardized, especially for fungal communities, and those available may produce contrasting results. While some pipelines cluster sequences based on a specified percentage of base pair similarity into operational taxonomic units (OTUs), others utilize denoising techniques to infer amplicon sequencing variants (ASVs). While ASVs are now considered a more accurate representation of taxonomic diversity for prokaryote communities based on 16S rRNA amplicon sequencing, the applicability of this method for fungal ITS sequences is still debated.
RESULTS: Here we compared the performance of two commonly used pipelines DADA2 (inferring ASVs) and mothur (clustering OTUs) on fungal metabarcoding sequences originating from two different environmental sample types (fresh bovine feces and pasture soil). At a 99% OTU similarity threshold, mothur consistently identified a higher fungal richness compared to DADA2. In addition, mothur generated homogenous relative abundances across multiple technical replicates (n = 18), while DADA2 results for the same replicates were highly heterogeneous.
CONCLUSIONS: Our study highlights a potential pipeline-associated bias in fungal metabarcoding data analysis of environmental samples. Based on the homogeneity of relative abundances across replicates and the capacity to detect OTUs/ASVs, we suggest using OTU clustering with a similarity of 97% as the most appropriate option for processing fungal metabarcoding data.}, }
@article {pmid39541885, year = {2024}, author = {Wang, G and Li, X and Deng, J and Cao, J and Meng, H and Dong, J and Zhang, H}, title = {Assessing soil cadmium quality standards for different land use types: A global synthesis.}, journal = {Journal of hazardous materials}, volume = {480}, number = {}, pages = {136450}, doi = {10.1016/j.jhazmat.2024.136450}, pmid = {39541885}, issn = {1873-3336}, abstract = {The contamination of cadmium (Cd) in soil has become an increasingly serious issue worldwide, presenting significant risks to human health, crop safety, and ecosystems. Despite its importance, there is a lack of standardized soil threshold values for use in regulating exposure to Cd-contaminated surface soil. By synthesizing soil environmental standards for Cd from 61 countries and 75 regions, this study analyzed and categorized these standards by land use types. The distribution of Cd quality standards among various countries was determined, based on available data primarily from the United States, Canada, Europe, Australia, and China. The established soil Cd quality standards were also determined for different land types, including lands for agricultural, residential, industrial, construction, commercial uses, and parks/green spaces. Using the ecological environment criteria - species sensitivity distribution (ECC-SSD) model, Cd levels were analyzed across different land use types, and it was determined that a log-logistic distribution was the best fitted model. Our findings indicated that soil Cd quality standards ranged from 0.11 to 5.20 mg/kg for agricultural land, 1.25 to 171.51 mg/kg for residential land, and 2.58 to 1845.26 mg/kg for industrial land, all within the 5-95 % percentile range. The 5 % hazard concentration (HC5) value was recommended as the latest national quality standards for each land type. This comprehensive assessment of global soil Cd quality standards provides valuable insight for decision-makers tasked with effectively managing and mitigating Cd pollution in soil.}, }
@article {pmid39539549, year = {2024}, author = {Pappa, T and Rivas, AL and Iandiorio, MJ and Hoogesteijn, AL and Fair, JM and Rojas Gil, AP and Burriel, AR and Bagos, PG and Chatzipanagiotou, S and Ioannidis, A}, title = {Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1430972}, pmid = {39539549}, issn = {1664-3224}, mesh = {Humans ; *Sepsis/immunology/mortality/blood/diagnosis ; Male ; Female ; Middle Aged ; Aged ; *Precision Medicine ; Leukocyte Count ; Biomarkers/blood ; Aged, 80 and over ; Adult ; Immunosuppression Therapy ; }, abstract = {INTRODUCTION: Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis.
METHODS: Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions.
RESULTS: The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named 'early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other'). Mortality data validated these labels: both 'suppression' subsets revealed 100% mortality, the 'immunocompetence' group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the 'intermediary' suppression expressed an impaired monocyte-related function, the 'late' suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine.
DISCUSSION: The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the 'other' group, additional studies are recommended.}, }
@article {pmid39537861, year = {2024}, author = {Noria, SF and Pratt, KJ and Abdel-Rasoul, M and Diaz, K and Shalash, B and Abul-Khoudoud, D and Needleman, B and Magallanes, M}, title = {The impact of social determinants of health (SDOH) on completing bariatric surgery at a single academic institution.}, journal = {Surgical endoscopy}, volume = {}, number = {}, pages = {}, pmid = {39537861}, issn = {1432-2218}, abstract = {BACKGROUND: Underutilization of bariatric surgery is multifactorial. This study aimed to understand the association of SDOH on not achieving surgery.
METHODS: 1081 applications for primary MBS from January-December 2021 were stratified into those that completed surgery (COM; n = 415), in progress > 1-year (IP; n = 107), dropped out (DO; n = 379), and never started (NS; n = 180). Using the American-Community-Survey results (2015-2020) and patient zip-codes, population differences in 4-domains of SDOH (demographic/social/housing/economic) were examined between COM versus the other groups. Additionally, using institutional MBSAQIP and EMR data, patient-specific differences in comorbidities were evaluated for COM versus IP/DO. Univariate analysis using Kruskal-Wallis, chi-squared/Fisher's exact tests were used for continuous and/or categorical variables. For patient-level analysis multinomial logistic regression was used to determine predictors of not achieving surgery. Hypothesis testing was conducted at an overall 5 percent type-I error rate (alpha = 0.05) and Bonferroni's method was used to adjust for multiple comparisons.
RESULTS: Compared to COM, IP-patients resided in zip-codes characterized by fewer married people (43% vs 46%; p = 0.019), lower education levels (49% vs 43%; p = 0.048), more households where rent was > 50% of household income (10% vs 8%, p = 0.002), and households below the poverty line (17.6% vs 14.5%, p = 0.017). At the patient-level, IP were more likely to be male (27.9% vs 14.9%; p = 0.014), publicly insured (44.9% vs 28.4%; p = 0.004), Black (35.5% vs 22.2%; p = 0.006), an active smoker (8.9% vs 2.2%; p = 0.018), have a higher BMI (49.6 vs 47.6; p = 0.01), and coronary intervention (5.8% vs 1.7%, p = 0.034). Comparison of COM vs DO was similar for both phases. Multinomial multivariable logistic regression demonstrated higher BMI (OR = 1.03,[CI]:1.01-1.05, p = 0.001), males (OR = 1.9,[CI]:1.09-3.32, p = 0.024), smoking (OR = 4.58,[CI]:1.74-12.02, p = 0.002), and Medicaid (OR = 2.16,[CI]:1.33-3.49, p = 0.002) independently predicted not achieving surgery.
CONCLUSION: Patient-level data demonstrated social not clinical factors predicted surgery completion. Given zip-codes characterizing the IP/DO groups had a greater prevalence of social risk, more attention needs to be directed patient-level social risks.}, }
@article {pmid39537735, year = {2024}, author = {Ki, J and Lee, JM and Lee, W and Kim, JH and Jin, H and Jung, S and Lee, J}, title = {Dual-encoder architecture for metal artifact reduction for kV-cone-beam CT images in head and neck cancer radiotherapy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27907}, pmid = {39537735}, issn = {2045-2322}, support = {NRF-2020R1F1A1073430//National Research Foundation of Korea/ ; NRF-2021R1F1A1057818//National Research Foundation of Korea/ ; HI21C1161//Korea Health Industry Development Institute/ ; RS-2020-II201336//Ministry of Science and ICT, South Korea/ ; }, mesh = {*Cone-Beam Computed Tomography/methods ; Humans ; *Head and Neck Neoplasms/radiotherapy/diagnostic imaging ; *Artifacts ; *Metals/chemistry ; Deep Learning ; Image Processing, Computer-Assisted/methods ; Radiotherapy Planning, Computer-Assisted/methods ; Radiotherapy Dosage ; Phantoms, Imaging ; }, abstract = {During a radiotherapy (RT) course, geometrical variations of target volumes, organs at risk, weight changes (loss/gain), tumor regression and/or progression can significantly affect the treatment outcome. Adaptive RT has become the effective methods along with technical advancements in imaging modalities including cone-beam computed tomography (CBCT). Planning CT (pCT) can be modified via deformable image registration (DIR), which is applied to the pair of pCT and CBCT. However, the artifact existed in both pCT and CBCT is a vulnerable factor in DIR. The dose calculation on CBCT is also suggested. Missing information due to the artifacts hinders the accurate dose calculation on CBCT. In this study, we aim to develop a deep learning-based metal artifact reduction (MAR) model to reduce the metal artifacts in CBCT for head and neck cancer RT. To train the proposed MAR model, we synthesized the kV-CBCT images including metallic implants, with and without metal artifacts (simulated image data pairs) through sinogram image handling process. We propose the deep learning architecture which focuses on both artifact removal and reconstruction of anatomic structure using a dual-encoder architecture. We designed four single-encoder models and three dual-encoder models based on UNet (for an artifact removal) and FusionNet (for a tissue restoration). Each single-encoder model contains either UNet or FusionNet, while the dual-encoder models have both UNet and FusionNet architectures. In the dual-encoder models, we implemented different feature fusion methods, including simple addition, spatial attention, and spatial/channel wise attention. Among the models, a dual-encoder model with spatial/channel wise attention showed the highest scores in terms of peak signal-to-noise ratio, mean squared error, structural similarity index, and Pearson correlation coefficient. CBCT images from 34 head and neck cancer patients were used to test the developed models. The dual-encoder model with spatial/channel wise attention showed the best results in terms of artifact index. By using the proposed model to CBCT, one can achieve more accurate synthetic pCT for head and neck patients as well as better tissue recognition and structure delineation for CBCT image itself.}, }
@article {pmid39537340, year = {2024}, author = {Di Battista, V and Danielsen, PH and Gajewicz-Skretna, A and Kedziorski, A and Seiffert, SB and Ma-Hock, L and Berthing, T and Mortensen, A and Sundermann, A and Skjolding, LM and Vogel, U and Baun, A and Wohlleben, W}, title = {Oxide-Perovskites for Automotive Catalysts Biotransform and Induce Multicomponent Clearance and Hazard.}, journal = {ACS nano}, volume = {18}, number = {47}, pages = {32672-32693}, pmid = {39537340}, issn = {1936-086X}, mesh = {*Oxides/chemistry ; Animals ; Catalysis ; *Lanthanum/chemistry ; Rats ; Mice ; Calcium Compounds/chemistry ; Titanium/chemistry ; Automobiles ; Male ; Biotransformation ; Surface Properties ; Lung/metabolism/drug effects ; }, abstract = {Oxide-perovskites designed for automotive catalysts contain multiple metal elements whose presence is crucial to achieving the targeted performance. They are highly stable in exhaust operating conditions; however, little is known about their stability under physiological conditions. As some of the metallic components are hazardous to humans and the environment, perovskite benefits in cleaner air must be balanced with risks in a Safe and Sustainable Design (SSbD) approach. New approach methodologies (NAMs), including in chemico and in silico methods, were used for testing hazards and benefits, including catalytic activity and tolerance for temporary excess of oxygen under dynamic driving conditions. The composition and surface properties of six different lanthanum-based oxide-perovskites compromised their stability under lung physiological conditions, influencing the oxidative damage of the particles and the bioacessibility of leaching metals. We found consistent biotransformation of the oxide-perovskite materials at pH 4.5. The leached lanthanum ions, but not other metals, respeciated into lanthanum phosphate nanoparticles, which increased the overall oxidative damage in additive synergy. The NAM results in the presented SSbD approach were challenged by in vivo studies in rats and mice, which confirmed multicomponent clearance from lungs into urine and supported the comparative ranking of effects against well-characterized spinel materials. Among the perovskites, the version with reduced nickel content and doped with palladium offered the best SSbD balance, despite not improving the conventional benchmark catalytic performance and related sustainability benefits. Redesign by industry may be necessary to better fulfill all SSbD dimensions.}, }
@article {pmid39536186, year = {2024}, author = {Corrêa-do-Nascimento, GS and Galvão, C and Leite, GR}, title = {Investigating the distribution of a rare Colombo-Venezuelan kissing bug, Rhodnius neivai, Lent, 1953, using geographical information system-based analyses.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {119}, number = {}, pages = {e240106}, pmid = {39536186}, issn = {1678-8060}, mesh = {Animals ; *Rhodnius ; *Geographic Information Systems ; Colombia ; *Insect Vectors/classification ; *Animal Distribution ; Venezuela ; Chagas Disease/transmission ; Ecosystem ; }, abstract = {BACKGROUND: Rhodnius neivai, a kissing bug found in the dry regions of Colombia and Venezuela, has limited documented occurrences. While it is not deemed a significant vector for Chagas disease, distributional and ecological studies are essential in monitoring species domiciliation and shedding light on the evolutionary aspects of the Rhodniini tribe.
OBJECTIVES: The study aims to provide a detailed revision of R. neivai distribution and evaluate general spatial data quality for ecological niche modelling (ENM). It will also provide the first published ENM for the species, which may aid species sampling and future analytical improvement.
METHODS: Registers and other spatial information were gathered by literature review; data georeferencing, preliminary geographical investigations, and model editing were conducted in GIS platforms; ENMs were built using R and explored the uncertainty of parameters and algorithms.
FINDINGS: Twenty four unique sites were identified, unearthing 17 previously uncovered records. Data lacks robust spatial and temporal precision; however, ENMs had acceptable validations. The models present some variation in suitability but with objective areas for sampling effort.
MAIN CONCLUSIONS: Rhodnius neivai distribution is better explained by conditions that characterise dry ecotypes, but further sampling is essential to improve modelling and advance with ecological and evolutive matters.}, }
@article {pmid39536049, year = {2024}, author = {Zhao, Y and Cordero, OX and Tikhonov, M}, title = {Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function.}, journal = {PLoS computational biology}, volume = {20}, number = {11}, pages = {e1012590}, pmid = {39536049}, issn = {1553-7358}, mesh = {*Algorithms ; Linear Models ; *Ecosystem ; *Computational Biology/methods ; Models, Biological ; Microbiota/physiology ; Nonlinear Dynamics ; }, abstract = {Microbial communities play key roles across diverse environments. Predicting their function and dynamics is a key goal of microbial ecology, but detailed microscopic descriptions of these systems can be prohibitively complex. One approach to deal with this complexity is to resort to coarser representations. Several approaches have sought to identify useful groupings of microbial species in a data-driven way. Of these, recent work has claimed some empirical success at de novo discovery of coarse representations predictive of a given function using methods as simple as a linear regression, against multiple groups of species or even a single such group (the ensemble quotient optimization (EQO) approach). Modeling community function as a linear combination of individual species' contributions appears simplistic. However, the task of identifying a predictive coarsening of an ecosystem is distinct from the task of predicting the function well, and it is conceivable that the former could be accomplished by a simpler methodology than the latter. Here, we use the resource competition framework to design a model where the "correct" grouping to be discovered is well-defined, and use synthetic data to evaluate and compare three regression-based methods, namely, two proposed previously and one we introduce. We find that regression-based methods can recover the groupings even when the function is manifestly nonlinear; that multi-group methods offer an advantage over a single-group EQO; and crucially, that simpler (linear) methods can outperform more complex ones.}, }
@article {pmid39530726, year = {2024}, author = {Toledo, MJL and Zawadzki, MJ and Scott, SB and Johnson, JA and Marcusson-Clavertz, D and Kim, J and Lanza, S and Almeida, DM and Sliwinski, MJ and Smyth, JM}, title = {Exploring the Utility of a Real-Time Approach to Characterising Within-Person Fluctuations in Everyday Stress Responses.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {6}, pages = {e3501}, pmid = {39530726}, issn = {1532-2998}, support = {/NH/NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; *Stress, Psychological/psychology ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; Aged ; }, abstract = {Few studies have measured components of stress responses in real time-an essential step in designing just-in-time interventions targeting moments of risk. Using ecological momentary assessment (EMA), we characterised stress response components to everyday stressors, including reactivity (the response following a stressor), recovery (the return towards baseline), and pile-up (the accumulation of stressors) (RRPs) by quantifying the dynamics of response indicators (i.e., subjective stress, negative affect, and perseverative cognition). To determine the utility of these novel measures in capturing and characterising acute moments of the stress response, this study evaluated the proportion of variance in RRPs attributed to (1) between-person, (2) between-days, and (3) within-day (momentary) levels. Healthy adults (n = 123; aged 35-65, 79% women, 91% non-Hispanic White) participated in a 14-day study assessing stress response via EMA 6 times a day. RRPs were constructed from 10,065 EMA reports. Multilevel models with moments nested within days nested within persons were used to partition variance in the RRPs. Reactivity and recovery indicators captured the most variation within-days (i.e., across moments; range 76%-80% and 87%-89%, respectively), with small amounts of variance between-person. For pile-up, variation was mostly observed between-days (range 60%-63%) and between-persons (range 27%-31%). In contrast, raw measures of stress response reflected substantial between-person (range 32%-54%) and within-day (range 34%-53%) variance. These results demonstrated that a person-specific approach to measuring stress response components (i.e., RRPs) can capture the dynamic within-person variation in stress response, as it occurs in real time, making it well-suited for use in novel just-in-time interventions targeting moments of risk.}, }
@article {pmid39526854, year = {2024}, author = {Tan, X and Xue, F and Zhang, C and Wang, T}, title = {mbDriver: identifying driver microbes in microbial communities based on time-series microbiome data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39526854}, issn = {1477-4054}, support = {12331009//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; }, abstract = {Alterations in human microbial communities are intricately linked to the onset and progression of diseases. Identifying the key microbes driving these community changes is crucial, as they may serve as valuable biomarkers for disease prevention, diagnosis, and treatment. However, there remains a need for further research to develop effective methods for addressing this critical task. This is primarily because defining the driver microbe requires consideration not only of each microbe's individual contributions but also their interactions. This paper introduces a novel framework, called mbDriver, for identifying driver microbes based on microbiome abundance data collected at discrete time points. mbDriver comprises three main components: (i) data preprocessing of time-series abundance data using smoothing splines based on the negative binomial distribution, (ii) parameter estimation for the generalized Lotka-Volterra (gLV) model using regularized least squares, and (iii) quantification of each microbe's contribution to the community's steady state by manipulating the causal graph implied by gLV equations. The performance of nonparametric spline-based denoising and regularized least squares estimation is comprehensively evaluated on simulated datasets, demonstrating superiority over existing methods. Furthermore, the practical applicability and effectiveness of mbDriver are showcased using a dietary fiber intervention dataset and an ulcerative colitis dataset. Notably, driver microbes identified in the dietary fiber intervention dataset exhibit significant effects on the abundances of short-chain fatty acids, while those identified in the ulcerative colitis dataset show a significant correlation with metabolism-related pathways.}, }
@article {pmid39526196, year = {2024}, author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Pale November moth, Epirrita christyi (Allen, 1906).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {540}, pmid = {39526196}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Pale November moth, Epirrita christyi (Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 474.20 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.99 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,983 protein-coding genes.}, }
@article {pmid39521320, year = {2024}, author = {Coelho, LA and Gonzalez, CLR and Tammurello, C and Campus, C and Gori, M}, title = {Hand and foot overestimation in visually impaired human adults.}, journal = {Neuroscience}, volume = {563}, number = {}, pages = {74-83}, doi = {10.1016/j.neuroscience.2024.10.055}, pmid = {39521320}, issn = {1873-7544}, mesh = {Humans ; Female ; Male ; Adult ; *Hand ; *Foot ; Middle Aged ; *Blindness/physiopathology/psychology ; Visually Impaired Persons/psychology ; Body Image/psychology ; Young Adult ; Sex Characteristics ; }, abstract = {Previous research has shown that visual impairment results in reduced audio, tactile and proprioceptive ability. One hypothesis is that these issues arise from inaccurate body representations. Few studies have investigated metric body representations in a visually impaired population. We designed an ecologically valid behavioural task in which visually impaired adults haptically explored various sized gloves or shoes. They were asked to indicate if they perceived each clothing item as bigger than the size of their hand or foot. In the post-hoc analyses we fit psychometric curves to the data to extract the point of subjective equality. We then compared the results to age/sex matched controls. We hypothesized the blind participants body representations should be more distorted. Because previous research has shown that females are more likely to overestimate body size, we predicted sex differences in the sighted participants. However, because blind adults have no exposure to visual ideals of body size, we predicted that there would be no sex differences. Our results showed thatblind participants overestimated their hands and feetto a similar degree. Sighted controls overestimated their hands significantly more than their feet. Taken together, our results partially support our hypothesis and suggest that visual deprivation, even for short periods result in hand size overestimation.}, }
@article {pmid39520764, year = {2025}, author = {Rodriguez-Caturla, MY and Margalho, LP and Graça, JS and Pia, AKR and Xavier, VL and Noronha, MF and Cabral, L and Lemos-Junior, WJF and Castillo, CJC and SantˈAna, AS}, title = {Bacterial dynamics and volatile metabolome changes of vacuum-packaged beef with different pH during chilled storage.}, journal = {International journal of food microbiology}, volume = {427}, number = {}, pages = {110955}, doi = {10.1016/j.ijfoodmicro.2024.110955}, pmid = {39520764}, issn = {1879-3460}, mesh = {*Volatile Organic Compounds/analysis/metabolism ; Hydrogen-Ion Concentration ; Vacuum ; Cattle ; Animals ; *Red Meat/microbiology ; *Food Packaging/methods ; *Food Microbiology ; *Food Storage ; Bacteria/metabolism/growth & development/classification/genetics/isolation & purification ; Metabolome ; Brazil ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study aimed to assess the growth of spoilage bacteria in Brazilian vacuum-packed beef across different pH ranges (5.4-5.8, 5.8-6.1, ≥6.1) stored at temperatures of 0 °C, 4 °C, and 7 °C. Additionally, the research sought to identify predominant spoilage bacteria at the genus level using 16S rDNA gene sequencing and analyze the principal volatile organic compounds (VOCs) produced by this microbiota through HS-SPME/GC-MS. Lactic acid bacteria (LAB) consistently exhibited counts exceeding 6.0 Log CFU/g, regardless of temperature and pH conditions. The bacterial diversity in the meat samples reflected the influence of slaughterhouse environments, with Pseudomonas and Serratia remaining dominant across different cuts and pH levels. Post-storage, variations in pH and temperature modulated the initial bacterial diversity, leading to a reduction in diversity and an increase in LAB such as Lactobacillus, Lactococcus, Leuconostoc, and Carnobacterium. Notably, these changes were observed within pH ranges of 5.4-5.8 and 5.8-6.1, irrespective of beef cuts and storage temperatures. Based on high throughput sequencing and VOCS, correlation analysis revealed a relationship between the growth of specific spoilage microorganisms under vacuum conditions and the presence of VOCs such as alcohols (e.g., 1-propanol, 2-methyl-) and ketones (e.g., 2-nonanone, 2-octanone, 2-heptanone), identifying them as potential indicators of spoilage bacteria growth.}, }
@article {pmid39516498, year = {2024}, author = {Weistuch, C and Murgas, KA and Zhu, J and Norton, L and Dill, KA and Tannenbaum, AR and Deasy, JO}, title = {Normal tissue transcriptional signatures for tumor-type-agnostic phenotype prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {27230}, pmid = {39516498}, issn = {2045-2322}, support = {BCRF-17-193//Breast Cancer Research Foundation/ ; W911NF2210292//Army Research Office/ ; FA9550-20-1-0029//Air Force Office of Scientific Research/ ; R01-AG048769/GF/NIH HHS/United States ; R01 AG048769/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Transcriptome ; *Phenotype ; *Gene Expression Regulation, Neoplastic ; Female ; Neoplasms/genetics/pathology/metabolism ; Gene Expression Profiling ; Breast Neoplasms/genetics/pathology/metabolism ; }, abstract = {Cancer transcriptional patterns reflect both unique features and shared hallmarks across diverse cancer types, but whether differences in these patterns are sufficient to characterize the full breadth of tumor phenotype heterogeneity remains an open question. We hypothesized that these shared transcriptomic signatures reflect repurposed versions of functional tasks performed by normal tissues. Starting with normal tissue transcriptomic profiles, we use non-negative matrix factorization to derive six distinct transcriptomic phenotypes, called archetypes, which combine to describe both normal tissue patterns and variations across a broad spectrum of malignancies. We show that differential enrichment of these signatures correlates with key tumor characteristics, including overall patient survival and drug sensitivity, independent of clinically actionable DNA alterations. Additionally, we show that in HR+/HER2- breast cancers, metastatic tumors adopt transcriptomic signatures consistent with the invaded tissue. Broadly, our findings suggest that cancer often arrogates normal tissue transcriptomic characteristics as a component of both malignant progression and drug response. This quantitative framework provides a strategy for connecting the diversity of cancer phenotypes and could potentially help manage individual patients.}, }
@article {pmid39512488, year = {2024}, author = {Lewis, JH and Kojima, H and Suenaga, M and Petsopoulos, D and Fujisawa, Y and Truong, XL and Warren, DL}, title = {The era of cybertaxonomy: X-ray microtomography reveals cryptic diversity and concealed cuticular sculpture in Aphanerostethus Voss, 1957 (Coleoptera, Curculionidae).}, journal = {ZooKeys}, volume = {1217}, number = {}, pages = {1-45}, pmid = {39512488}, issn = {1313-2989}, abstract = {Weevils represent one of the most speciose and economically important animal clades, but remain poorly studied across much of the Oriental Region. Here, an integrative revision of the Oriental, flightless genus Aphanerostethus Voss, 1957 (Curculionidae: Molytinae) based on X-ray microtomography, multi-gene DNA barcoding (CO1, Cytb, 16S), and traditional morphological techniques (light microscopy, dissections) is presented. Twelve new species, namely, A.armatus Lewis & Kojima, sp. nov., A.bifidus Kojima & Lewis, sp. nov., A.darlingi Lewis, sp. nov., A.decoratus Lewis & Kojima, sp. nov., A.falcatus Kojima, Lewis & Fujisawa, sp. nov., A.incurvatus Kojima & Lewis, sp. nov., A.japonicus Lewis & Kojima, sp. nov., A.magnus Lewis & Kojima, sp. nov., A.morimotoi Kojima & Lewis, sp. nov., A.nudus Lewis & Kojima, sp. nov., A.spinosus Lewis & Kojima, sp. nov., and A.taiwanus Lewis, Fujisawa & Kojima, sp. nov. are described from Japan, Taiwan, Vietnam, and Malaysia. A neotype is designated for A.vannideki Voss, 1957. The hitherto monotypic genus Darumazo Morimoto & Miyakawa, 1985, syn. nov. is synonymized under Aphanerostethus based on new morphological data and Aphanerostethusdistinctus (Morimoto & Miyakawa, 1985), comb. nov. is transferred accordingly. X-ray microtomography is successfully used to explore for stable interspecific differences in cuticular, internal and micro morphology. Remarkable species-specific sexual dimorphism in the metatibial uncus is described in seven of the newly described Aphanerostethus species and the evolution of this character is discussed.}, }
@article {pmid39511491, year = {2024}, author = {Tang, Y and Tian, C and Yao, D and Yang, S and Shi, L and Yi, L and Peng, Q}, title = {Community assembly and potential function analysis of the endophyte in Eucommia ulmoides.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {460}, pmid = {39511491}, issn = {1471-2180}, mesh = {*Endophytes/genetics/metabolism/classification/physiology/isolation & purification ; *Eucommiaceae/microbiology ; *Ascomycota/genetics/growth & development/physiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; High-Throughput Nucleotide Sequencing ; Iridoid Glucosides/metabolism ; Basidiomycota/genetics/physiology ; Symbiosis ; Fungi/classification/genetics/isolation & purification/metabolism/physiology ; Computational Biology ; }, abstract = {Endophytes play a pivotal role in protecting host plants from both biotic and abiotic stresses, promoting the production of active components (AC) and plant growth. However, the succession of the endophyte community in Eucommia ulmoides (E. ulmoides), particularly the community assembly and function, has not been extensively investigated. In this study, we employed high-throughput sequencing and bioinformatics tools to analyze endophyte diversity across different tree ages, parts, and periods. We examined the population differences, correlations, community assembly mechanisms, and functional roles of these endophytes. Functional predictions via PICRUSt2 revealed that most endophytic fungal functions were linked to biosynthesis, with significant differences in biosynthetic functional abundance across parts and periods. In contrast, the metabolic activity of endophytic bacteria remained stable across different periods and parts. Correlation analysis further confirmed a strong positive relationship between ACs and certain endophytic fungi. Among them, the fungal phyla Ascomycota and Basidiomycota were identified as key contributors to the metabolism of chlorogenic acid (CA), while Aucubin was significantly positively correlated with several endophytic bacteria. These findings provide valuable insights into the functional roles and community assembly mechanism of E. ulmoides endophytes, as well as their symbiotic relationships.}, }
@article {pmid39507254, year = {2024}, author = {Flores, M and Ho, E and Ly, C and Ceberio, N and Guardado, M and Felix, K and Thorner, HM and Paunovich, M and Godek, C and Kalaydjian, C and Rohlfs, RV}, title = {Decreased accuracy of forensic DNA mixture analysis for groups with lower genetic diversity.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111067}, pmid = {39507254}, issn = {2589-0042}, support = {T32 GM148332/GM/NIGMS NIH HHS/United States ; }, abstract = {Forensic investigation of DNA samples from multiple contributors has become commonplace. These complex analyses use statistical frameworks accounting for multiple levels of uncertainty in allelic contributions from different individuals, particularly for samples containing few molecules of DNA. These methods have been thoroughly tested along some axes of variation, but less attention has been paid to accuracy across human genetic variation. Here, we quantify the accuracy of DNA mixture analysis over 83 human groups. We find higher false inclusion rates for mixtures with more contributors and for groups with lower genetic diversity. Even for three-contributor mixtures where two contributors are known and the reference group is correctly specified, false inclusion rates are 1e-5 or higher for 36 out of 83 groups. This means that, depending on multiple testing, some false inclusions may be expected. These false positives could be lessened with more selective and conservative use of DNA mixture analysis.}, }
@article {pmid39503522, year = {2024}, author = {Campelo, F and de Oliveira, ALG and Reis-Cunha, J and Fraga, VG and Bastos, PH and Ashford, J and Ekárt, A and Adelino, TER and Silva, MVF and de Melo Iani, FC and de Jesus, ACP and Bartholomeu, DC and de Souza Trindade, G and Fujiwara, RT and Bueno, LL and Lobo, FP}, title = {Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39503522}, issn = {1477-4054}, support = {BIP-00123-23//FAPEMIG/ ; INCT-406441/2022-7//Brazilian National Institutes of Science and Technology/ ; RED-00067-23//Rede Mineira de Imunobiológicos/ ; APQ-4035/17//State of Minas Gerais Research Support Foundation/ ; 310311/2023-3//National Council for Scientific and Technological Development/ ; 405249/2022-5//MCTI/Brazil/ ; MR/T016019/1//UK Medical Research Council/ ; //EPSRC/UK/ ; }, mesh = {*Phylogeny ; Humans ; *Epitopes, B-Lymphocyte/immunology ; Orthopoxvirus/immunology/genetics ; Computational Biology/methods ; Vaccinia virus/immunology/genetics ; Mpox (monkeypox) ; }, abstract = {We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.}, }
@article {pmid39501271, year = {2024}, author = {Sijm-Eeken, M and Ossebaard, HC and Čaluković, A and Temme, B and Peute, LW and Jaspers, MW}, title = {Linking theory and practice to advance sustainable healthcare: the development of maturity model version 1.0.}, journal = {BMC health services research}, volume = {24}, number = {1}, pages = {1350}, pmid = {39501271}, issn = {1472-6963}, mesh = {Humans ; *Delivery of Health Care/organization & administration ; Climate Change ; Sustainable Development ; Conservation of Natural Resources/methods ; Models, Theoretical ; Models, Organizational ; }, abstract = {BACKGROUND: Climate change and increased awareness of planetary health have made reducing ecological footprints a priority for healthcare organizations. However, improving healthcare's environmental impact remains difficult. Numerous researchers argue these difficulties are caused by healthcare's environmental impact being multidimensional, influenced throughout the healthcare chain, and often has downstream consequences that are hard to identify or to measure. Even though existing research describes many successful approaches to reduce healthcare's environmental impact, a robust multidimensional framework to assess this impact is lacking. This research aims at developing a maturity model for sustainable healthcare that could be used for self-assessment by healthcare professionals to identify improvement actions and for sharing best practices in environmental sustainability.
METHODS: A design-oriented approach for maturity model development was combined with an expert panel and six case studies to develop, refine and expand the maturity model for environmentally sustainable healthcare.
RESULTS: A maturity model was developed containing four domains: 'Governance', 'Organization Structures', 'Processes', and 'Outcomes and Control'. Applying the model in real-world environments demonstrated the model's understandability, ease of use, usefulness, practicality and ability to identify improvement actions for environmental sustainability in healthcare organizations.
CONCLUSIONS: This study found that healthcare practitioners could apply the maturity model developed and tested in this study in several hours without training to help them gain valuable insights into the environment footprint of the healthcare setting they worked in. Systematically implementing the model developed in this study could help address the urgent need to mitigate the substantial environmental impact of healthcare. These implementations can help evaluate and improve the maturity model.}, }
@article {pmid39497067, year = {2024}, author = {Moeller, AH and Dillard, BA and Goldman, SL and Real, MVF and Sprockett, DD}, title = {Removal of sequencing adapter contamination improves microbial genome databases.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1033}, pmid = {39497067}, issn = {1471-2164}, mesh = {Animals ; *Databases, Genetic ; DNA Contamination ; Genome, Microbial ; Humans ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Cattle ; Mice ; Swine ; }, abstract = {Advances in assembling microbial genomes have led to growth of reference genome databases, which have been transformative for applied and basic microbiome research. Here we show that published microbial genome databases from humans, mice, cows, pigs, fish, honeybees, and marine environments contain significant sequencing-adapter contamination that systematically reduces assembly accuracy and contiguousness. By removing the adapter-contaminated ends of contiguous sequences and reassembling MGnify reference genomes, we improve the quality of assemblies in these databases.}, }
@article {pmid39494195, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Case-bearing Clothes moth, Tinea pellionella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {119}, pmid = {39494195}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Tinea pellionella (the Case-bearing Clothes moth; Arthropoda; Insecta; Lepidoptera; Tineidae). The genome sequence is 245.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 25.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,811 protein coding genes.}, }
@article {pmid39493766, year = {2024}, author = {Chakraborty, H and Chakraborty, HJ and Das, BK and Maity, J}, title = {Age-specific changes in the serum proteome of female anadromous, hilsa Tenualosa ilisha: a comparative analysis across developmental stages.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1448627}, pmid = {39493766}, issn = {1664-3224}, mesh = {Female ; *Proteome ; Animals ; Proteomics/methods ; Tandem Mass Spectrometry ; Protein Interaction Maps ; Computational Biology/methods ; Age Factors ; Chromatography, Liquid ; Blood Proteins/metabolism ; Fishes/genetics/blood ; Aging/blood/immunology ; }, abstract = {INTRODUCTION: The proteome profile of the female Tenualosa ilisha (Hamilton, 1822), a species of great ecological and economic importance, across various age groups was investigated to comprehend the functional dynamics of the serum proteome for conservation and aquaculture, as well as sustain the population.
METHODS: Advanced liquid chromatography-tandem mass spectrometry LC-MS/MS-based proteomic data were analysed and submitted to the ProteomeXchange Consortium via PRIDE (PRoteomics IDEntifications database). Bioinformatics analysis of serum proteome have been done and it showed different proteins associated with GO Gene Ontology () terms, and the genes associated with enriched KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways (such as phagosome, mTOR, Apelin signalling pathways, herpes simplex virus) implicated in immune responses.
RESULTS: The expression levels of important immunological proteins, such as those involved in cellular defence and inflammatory responses, were significantly different age-dependently. In this study, we annotated 952, 494, 415, and 282 proteins in year classes IV, III, II, and I Hilsa, respectively, and analysed their Protein-Protein Interaction (PPI) networks based on their functional characteristics. From year classes I to IV, new proteins appeared and were more than three-fold. Notably, class I hilsa displayed a lower abundance of proteins than class IV hilsa.
DISCUSSION: This is the first study, to the best of our knowledge, to report the analysis of the serum proteome of hilsa at different developmental stages, and the results can help improve the understanding of the mechanisms underlying the different changes in protein enrichment during migration in hilsa. This analysis also offers crucial insights into the immune system for hilsa conservation and management.}, }
@article {pmid39493638, year = {2024}, author = {Reuken, PA and Besteher, B and Bleidorn, J and Brockmann, D and Finke, K and Freytag, A and Lehmann-Pohl, K and Lemhöfer, C and Mikolajczyk, R and Puta, C and Scherag, A and Wiedermann, M and Zippel-Schultz, B and Stallmach, A}, title = {Web-based telemedicine approach for treatment of post-COVID-19 in Thuringia (WATCH).}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241291748}, pmid = {39493638}, issn = {2055-2076}, abstract = {OBJECTIVE: After infection with SARS-CoV-2, a substantial proportion of patients develop long-lasting sequelae. These sequelae include fatigue (potentially as severe as that seen in ME/CFS cases), cognitive dysfunction, and psychiatric symptoms. Because the pathophysiology of these sequelae remains unclear, existing therapeutic concepts address the symptoms through pacing strategies, cognitive training, and psychological therapy.
METHODS: Here, we present a protocol for a digital multimodal structured intervention addressing common symptoms through three intervention modules: BRAIN, BODY, and SOUL. This intervention includes an assessment conducted via a mobile "post-COVID-19 bus" near the patient's home, as well as the use of wearable devices and mobile applications to support pacing strategies and collection of data, including ecological momentary assessment.
RESULTS: We will focus on physical component subscore of the SF36 as Quality of Life parameter as the primary outcome parameter for WATCH to take into account the holistic approach that is necessary for care of post-COVID patients.
CONCLUSION: In the current project, we present a protocol for a holistic and multimodal structured therapeutic concept which is easily accessible, and scalable for post-COVID patients.}, }
@article {pmid39488960, year = {2024}, author = {Tayyab, M and Hussain, M and Zhang, J and Ullah, S and Tong, Z and Rahman, ZU and Al-Aizari, AR and Al-Shaibah, B}, title = {Leveraging GIS-based AHP, remote sensing, and machine learning for susceptibility assessment of different flood types in peshawar, Pakistan.}, journal = {Journal of environmental management}, volume = {371}, number = {}, pages = {123094}, doi = {10.1016/j.jenvman.2024.123094}, pmid = {39488960}, issn = {1095-8630}, mesh = {*Floods ; Pakistan ; *Machine Learning ; *Geographic Information Systems ; Algorithms ; Remote Sensing Technology ; }, abstract = {Due to its diverse topography, Pakistan faces different types of floods each year, which cause substantial physical, environmental, and socioeconomic damage. However, the susceptibility of specific regions to different flood types remains unexplored. To the best of our knowledge for the first time, this study employed an integrated approach by leveraging a GIS-based Analytical Hierarchy Process (AHP), remote sensing, and machine learning (ML) algorithms, to assess susceptibility to three different types of flooding in Peshawar, Pakistan. The study first evaluated the degree of susceptibility to riverine, urban, and flash floods using the GIS-based AHP technique, and then employed ML models, (i.e., specifically Random Forest [RF] and Extreme Gradient Boosting [XG-Boost] to analyze multi-type flood susceptibility in the study region. The performance of the ML models was also evaluated, and the XG-Boost model outperforms RF, demonstrating a higher correlation coefficient (R[2] = 0.561-0.922) and lower mean absolute error (MAE = 0.042-0.354), and root-mean-square error (RMSE = 0.119-0.415) for both training and testing datasets. The superior performance of the XG-Boost was further confirmed by the higher value of the area under the curve (AUC) values, which is relatively higher (0.87) than that of the AHP (0.70) and RF (0.86) models. Based on the relative best performance, the XG-Boost model was chosen for further susceptibility assessment of different types of floods, and the generated flood susceptibility maps revealed that 20.9% of the total area is susceptible to riverine flooding, while 30.27% and 48.68% of the total area is susceptible to urban and flash flooding, respectively. The study's findings are significant, offering valuable insights for relevant stakeholders in guiding future flood risk management and sustainable land use plans in the study area.}, }
@article {pmid39480949, year = {2024}, author = {Goldshtein, A and Chen, X and Amichai, E and Boonman, A and Harten, L and Yinon, O and Orchan, Y and Nathan, R and Toledo, S and Couzin, ID and Yovel, Y}, title = {Acoustic cognitive map-based navigation in echolocating bats.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6721}, pages = {561-567}, doi = {10.1126/science.adn6269}, pmid = {39480949}, issn = {1095-9203}, mesh = {Animals ; Acoustics ; *Chiroptera/physiology ; *Cognition ; *Echolocation ; Geographic Information Systems ; Homing Behavior ; *Spatial Navigation ; }, abstract = {Bats are known for their ability to use echolocation for obstacle avoidance and orientation. However, the extent to which bats utilize their highly local and directional echolocation for kilometer-scale navigation is unknown. In this study, we translocated wild Kuhl's pipistrelle bats and tracked their homing abilities while manipulating their visual, magnetic, and olfactory sensing and accurately tracked them using a new reverse GPS system. We show that bats can identify their location after translocation and conduct several-kilometer map-based navigation using solely echolocation. This proposition was further supported by a large-scale echolocation model disclosing how bats use environmental acoustic information to perform acoustic cognitive map-based navigation. We also demonstrate that navigation is improved when using both echolocation and vision.}, }
@article {pmid39480880, year = {2024}, author = {Silva, GAA and Harder, AM and Kirksey, KB and Mathur, S and Willoughby, JR}, title = {Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012566}, pmid = {39480880}, issn = {1553-7358}, mesh = {*Homozygote ; *Genetics, Population/methods ; *Inbreeding ; Animals ; Models, Genetic ; Computational Biology/methods ; Humans ; Computer Simulation ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.}, }
@article {pmid39480818, year = {2024}, author = {Ramesh, S and Rapp, S and Tapias Gomez, J and Levine, B and Tapias-Gomez, D and Chung, D and Truong, Z}, title = {Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.}, journal = {PloS one}, volume = {19}, number = {10}, pages = {e0309707}, pmid = {39480818}, issn = {1932-6203}, mesh = {*User-Computer Interface ; *Software ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Databases, Nucleic Acid ; Web Browser ; }, abstract = {Land managers, researchers, and regulators increasingly utilize environmental DNA (eDNA) techniques to monitor species richness, presence, and absence. In order to properly develop a biological assay for eDNA metabarcoding or quantitative PCR, scientists must be able to find not only reference sequences (previously identified sequences in a genomics database) that match their target taxa but also reference sequences that match non-target taxa. Determining which taxa have publicly available sequences in a time-efficient and accurate manner currently requires computational skills to search, manipulate, and parse multiple unconnected DNA sequence databases. Our team iteratively designed a Graphic User Interface (GUI) Shiny application called the Reference Sequence Browser (RSB) that provides users efficient and intuitive access to multiple genetic databases regardless of computer programming expertise. The application returns the number of publicly accessible barcode markers per organism in the NCBI Nucleotide, BOLD, or CALeDNA CRUX Metabarcoding Reference Databases. Depending on the database, we offer various search filters such as min and max sequence length or country of origin. Users can then download the FASTA/GenBank files from the RSB web tool, view statistics about the data, and explore results to determine details about the availability or absence of reference sequences.}, }
@article {pmid39483086, year = {2024}, author = {Behera, BP and Naik, H and Konkimalla, VB}, title = {Peptaloid: A Comprehensive Database for Exploring Peptide Alkaloid.}, journal = {Journal of chemical information and modeling}, volume = {64}, number = {22}, pages = {8387-8395}, doi = {10.1021/acs.jcim.4c01667}, pmid = {39483086}, issn = {1549-960X}, mesh = {*Peptides/chemistry ; *Alkaloids/chemistry/pharmacology ; Databases, Protein ; Machine Learning ; Databases, Factual ; Humans ; }, abstract = {Peptaloid is the first dedicated database for peptide alkaloid molecules, a unique class of naturally derived compounds known for their structural diversity and significant biological activities. Despite their promising potential in drug discovery and therapeutic development, research on peptide alkaloids has been limited by the absence of a comprehensive and centralized resource. Fragmented data across various sources have posed a significant challenge, underscoring the need for a specialized database to facilitate more efficient research and application. Peptaloid addresses this critical gap by providing a database with over 161,000 peptide alkaloid entries, each detailed with structural, physicochemical, and pharmacological properties. By leveraging advanced computational tools and machine learning, Peptaloid generates ADMET profiles, aiding in identifying and optimizing therapeutic candidates. Designed for versatility, the database supports various applications beyond drug discovery, including ecology and material sciences. Peptaloid (as a specialized database for peptide alkaloids) will play a crucial role in innovation and collaboration across scientific disciplines. Peptaloid is accessible at https://peptaloid.niser.ac.in.}, }
@article {pmid39481332, year = {2025}, author = {Yao, M and Ren, A and Yang, X and Chen, L and Wang, X and van der Meer, W and van Loosdrecht, MCM and Liu, G and Pabst, M}, title = {Unveiling the influence of heating temperature on biofilm formation in shower hoses through multi-omics.}, journal = {Water research}, volume = {268}, number = {Pt B}, pages = {122704}, doi = {10.1016/j.watres.2024.122704}, pmid = {39481332}, issn = {1879-2448}, mesh = {*Biofilms ; Proteomics ; Heating ; Metagenomics ; Hot Temperature ; Metagenome ; Multiomics ; }, abstract = {Shower systems provide unique environments that are conducive to biofilm formation and the proliferation of pathogens. The water heating temperature is a delicate decision that can impact microbial growth, balancing safety and energy consumption. This study investigated the impact of different heating temperatures (39 °C, 45 °C, 51 °C and 58 °C) on the shower hose biofilm (exposed to a final water temperature of 39 °C) using controlled full-scale shower setups. Whole metagenome sequencing and metaproteomics were employed to unveil the microbial composition and protein expression profiles. Overall, the genes and enzymes associated with disinfectant resistance and biofilm formation appeared largely unaffected. However, metagenomic analysis revealed a sharp decline in the number of total (86,371 to 34,550) and unique genes (32,279 to 137) with the increase in hot water temperature, indicating a significant reduction of overall microbial complexity. None of the unique proteins were detected in the proteomics experiments, suggesting smaller variation among biofilms on the proteome level compared to genomic data. Furthermore, out of 43 pathogens detected by metagenomics, only 5 could actually be detected by metaproteomics. Most interestingly, our study indicates that 45 °C heating temperature may represent an optimal balance. It minimizes active biomass (ATP) and reduces the presence of pathogens while saving heating energy. Our study offered new insights into the impact of heating temperature on shower hose biofilm formation and proposed optimal parameters that ensure biosafety while conserving energy.}, }
@article {pmid39477106, year = {2024}, author = {Manzanedo, RD and Chin, ARO and Ettinger, AK and Pederson, N and Pradhan, K and Guiterman, CH and Su, J and Baumgarten, F and Hille Ris Lambers, J}, title = {Moving ecological tree-ring big data forwards: Limitations, data integration, and multidisciplinarity.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {177244}, doi = {10.1016/j.scitotenv.2024.177244}, pmid = {39477106}, issn = {1879-1026}, mesh = {*Ecology ; *Big Data ; *Trees ; *Databases, Factual ; Environmental Monitoring/methods ; Forests ; Ecosystem ; }, abstract = {In recent years, tree-ring databases have emerged as a remarkable resource for ecological research, allowing us to address ecological questions at unprecedented temporal and spatial scales. However, concerns regarding big tree-ring data limitations and risks have also surfaced, leading to questions about their potential to be representative of long-term forest responses. Here, we highlight three paths of action to improve on tree-ring databases in ecology: 1) Implementing consistent bias analyses in large dendroecological databases and promoting community-driven data to address data limitations, 2) Encouraging the integration of tree-ring data with other ecological datasets, and 3) Promoting theory-driven, mechanistic dendroecological research. These issues are increasingly important for tackling pressing cross-disciplinary research questions. Finally, although we focus here on tree ring databases, these points apply broadly across many aggregative databases in ecology.}, }
@article {pmid39475652, year = {2024}, author = {Chala, D and Endresen, D and Demissew, S and Slaughter, LA and Johnsen, EB and Stenseth, NC}, title = {Stop using racist, unethical, and inappropriate names in taxonomy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {45}, pages = {e2415490121}, pmid = {39475652}, issn = {1091-6490}, }
@article {pmid39473806, year = {2024}, author = {Ayadi, H and Elbéji, A and Despotovic, V and Fagherazzi, G}, title = {Digital Vocal Biomarker of Smoking Status Using Ecological Audio Recordings: Results from the Colive Voice Study.}, journal = {Digital biomarkers}, volume = {8}, number = {1}, pages = {159-170}, pmid = {39473806}, issn = {2504-110X}, abstract = {INTRODUCTION: The complex health, social, and economic consequences of tobacco smoking underscore the importance of incorporating reliable and scalable data collection on smoking status and habits into research across various disciplines. Given that smoking impacts voice production, we aimed to develop a gender and language-specific vocal biomarker of smoking status.
METHODS: Leveraging data from the Colive Voice study, we used statistical analysis methods to quantify the effects of smoking on voice characteristics. Various voice feature extraction methods combined with machine learning algorithms were then used to produce a gender and language-specific (English and French) digital vocal biomarker to differentiate smokers from never-smokers.
RESULTS: A total of 1,332 participants were included after propensity score matching (mean age = 43.6 [13.65], 64.41% are female, 56.68% are English speakers, 50% are smokers and 50% are never-smokers). We observed differences in voice features distribution: for women, the fundamental frequency F0, the formants F1, F2, and F3 frequencies and the harmonics-to-noise ratio were lower in smokers compared to never-smokers (p < 0.05) while for men no significant disparities were noted between the two groups. The accuracy and AUC of smoking status prediction reached 0.71 and 0.76, respectively, for the female participants, and 0.65 and 0.68, respectively, for the male participants.
CONCLUSION: We have shown that voice features are impacted by smoking. We have developed a novel digital vocal biomarker that can be used in clinical and epidemiological research to assess smoking status in a rapid, scalable, and accurate manner using ecological audio recordings.}, }
@article {pmid39473051, year = {2024}, author = {Wang, Y and Chen, J and Ni, Y and Liu, Y and Gao, X and Tse, MA and Panagiotou, G and Xu, A}, title = {Exercise-changed gut mycobiome as a potential contributor to metabolic benefits in diabetes prevention: an integrative multi-omics study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2416928}, pmid = {39473051}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Exercise ; Middle Aged ; *Mycobiome ; *Fungi/classification/genetics/isolation & purification ; *Feces/microbiology ; Proteomics ; Prediabetic State/microbiology/metabolism ; Metabolomics ; Bacteria/classification/isolation & purification/genetics/metabolism ; Adult ; Diabetes Mellitus, Type 2/microbiology/prevention & control ; Metagenomics ; Multiomics ; }, abstract = {BACKGROUND: The importance of gut microbes in mediating the benefits of lifestyle intervention is increasingly recognized. However, compared to the bacterial microbiome, the role of intestinal fungi in exercise remains elusive. With our established randomized controlled trial of exercise intervention in Chinese males with prediabetes (n = 39, ClinicalTrials.gov:NCT03240978), we investigated the dynamics of human gut mycobiome and further interrogated their associations with exercise-elicited outcomes using multi-omics approaches.
METHODS: Clinical variations and biological samples were collected before and after training. Fecal fungal composition was analyzed using the internal transcribed spacer 2 (ITS2) sequencing and integrated with paired shotgun metagenomics, untargeted metabolomics, and Olink proteomics.
RESULTS: Twelve weeks of exercise training profoundly promoted fungal ecological diversity and intrakingdom connection. We further identified exercise-responsive genera with potential metabolic benefits, including Verticillium, Sarocladium, and Ceratocystis. Using multi-omics approaches, we elucidated comprehensive associations between changes in gut mycobiome and exercise-shaped metabolic phenotypes, bacterial microbiome, and circulating metabolomics and proteomics profiles. Furthermore, a machine-learning algorithm built using baseline microbial signatures and clinical characteristics predicted exercise responsiveness in improvements of insulin sensitivity, with an area under the receiver operating characteristic (AUROC) of 0.91 (95% CI: 0.85-0.97) in the discovery cohort and of 0.79 (95% CI: 0.74-0.86) in the independent validation cohort (n = 30).
CONCLUSIONS: Our findings suggest that intense exercise training significantly remodels the human fungal microbiome composition. Changes in gut fungal composition are associated with the metabolic benefits of exercise, indicating gut mycobiome is a possible molecular transducer of exercise. Moreover, baseline gut fungal signatures predict exercise responsiveness for diabetes prevention, highlighting that targeting the gut mycobiome emerges as a prospective strategy in tailoring personalized training for diabetes prevention.}, }
@article {pmid39472185, year = {2024}, author = {Orr, MC and Albert, G and Hughes, AC and Koludarov, I and Luo, A and Qiao, H and Wang, MQ and Chesters, D and Zhu, CD}, title = {Dark data limit the biological sciences.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2024.10.021}, pmid = {39472185}, issn = {2095-9281}, }
@article {pmid39470965, year = {2024}, author = {Sandin, P and Baard, P and Bülow, W and Helgesson, G}, title = {Authorship and Citizen Science: Seven Heuristic Rules.}, journal = {Science and engineering ethics}, volume = {30}, number = {6}, pages = {53}, pmid = {39470965}, issn = {1471-5546}, support = {2019-00548//Svenska Forskningsrådet Formas/ ; }, mesh = {*Authorship/standards ; Humans ; *Citizen Science/ethics ; *Heuristics ; *Guidelines as Topic ; *Ethics, Research ; *Publishing/ethics/standards ; Editorial Policies ; Research Personnel/ethics ; Volunteers ; Social Responsibility ; }, abstract = {Citizen science (CS) is an umbrella term for research with a significant amount of contributions from volunteers. Those volunteers can occupy a hybrid role, being both 'researcher' and 'subject' at the same time. This has repercussions for questions about responsibility and credit, e.g. pertaining to the issue of authorship. In this paper, we first review some existing guidelines for authorship and their applicability to CS. Second, we assess the claim that the guidelines from the International Committee of Medical Journal Editors (ICMJE), known as 'the Vancouver guidelines', may lead to exclusion of deserving citizen scientists as authors. We maintain that the idea of including citizen scientists as authors is supported by at least two arguments: transparency and fairness. Third, we argue that it might be plausible to include groups as authors in CS. Fourth and finally, we offer a heuristic list of seven recommendations to be considered when deciding about whom to include as an author of a CS publication.}, }
@article {pmid39470730, year = {2024}, author = {Bağcı, C and Nuhamunada, M and Goyat, H and Ladanyi, C and Sehnal, L and Blin, K and Kautsar, SA and Tagirdzhanov, A and Gurevich, A and Mantri, S and von Mering, C and Udwary, D and Medema, MH and Weber, T and Ziemert, N}, title = {BGC Atlas: a web resource for exploring the global chemical diversity encoded in bacterial genomes.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkae953}, pmid = {39470730}, issn = {1362-4962}, support = {161L0284C//Federal Ministry of Research and Education (BMBF)/ ; TTU09.716//German Centre for Infection Research (DZIF)/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Saarland University/ ; //National Agri-Food Biotechnology Institute/ ; 101064285//Horizon Europe-Research and Innovation Framework Programme/ ; //Office of Science/ ; DE-AC02-05CH11231//Department of Energy/ ; }, abstract = {Secondary metabolites are compounds not essential for an organism's development, but provide significant ecological and physiological benefits. These compounds have applications in medicine, biotechnology and agriculture. Their production is encoded in biosynthetic gene clusters (BGCs), groups of genes collectively directing their biosynthesis. The advent of metagenomics has allowed researchers to study BGCs directly from environmental samples, identifying numerous previously unknown BGCs encoding unprecedented chemistry. Here, we present the BGC Atlas (https://bgc-atlas.cs.uni-tuebingen.de), a web resource that facilitates the exploration and analysis of BGC diversity in metagenomes. The BGC Atlas identifies and clusters BGCs from publicly available datasets, offering a centralized database and a web interface for metadata-aware exploration of BGCs and gene cluster families (GCFs). We analyzed over 35 000 datasets from MGnify, identifying nearly 1.8 million BGCs, which were clustered into GCFs. The analysis showed that ribosomally synthesized and post-translationally modified peptides are the most abundant compound class, with most GCFs exhibiting high environmental specificity. We believe that our tool will enable researchers to easily explore and analyze the BGC diversity in environmental samples, significantly enhancing our understanding of bacterial secondary metabolites, and promote the identification of ecological and evolutionary factors shaping the biosynthetic potential of microbial communities.}, }
@article {pmid39469132, year = {2024}, author = {Bernstein, JM and Bautista, JB and Clores, MA and Brown, RM and Ruane, S and Sanguila, MB and Alis-Besenio, MGJ and Pejo, CLF and Cuesta, MA}, title = {Using mangrove and field observation data to identify fine-scale species distributions: a case study in bockadams (Serpentes: Homalopsidae: Cerberus).}, journal = {Royal Society open science}, volume = {11}, number = {10}, pages = {240483}, pmid = {39469132}, issn = {2054-5703}, abstract = {Characterization of species distributions is a fundamental challenge in biodiversity science, with particular significance for downstream evolutionary studies, conservation efforts, field-based faunal studies and estimates of species diversity. Checklists and phylogenetic studies often focus on poorly known, rare taxa with limited ranges. However, studies of widely distributed, ecologically important species that are abundant in their preferred microhabitats are also important for systematics and local conservation efforts, but less often studied. We collected novel natural history data during fieldwork (2019-2023) for Philippine populations of bockadams (Homalopsidae: Cerberus), one of the most abundant vertebrates in Southeast Asian aquatic systems. Considered a coastal snake, many studies report Cerberus inland. We report the frequency of encounters of Cerberus schneiderii, and the IUCN data-deficient, Philippine-endemic Cerberus microlepis during six expeditions (62 days; 1041 person-hours). We report new occurrence data for 69 C. schneiderii and 6 C. microlepis for coastal and inland populations, water measurements and dietary observations. Regression analyses and ecological niche models show the importance of coastal and mangrove habitats for Cerberus. Our study is the most comprehensive assessment of Philippine Cerberus populations to date and provides critical baseline natural history data for downstream research on widespread and range-restricted species of Southeast Asian snakes.}, }
@article {pmid39469049, year = {2024}, author = {Chávez-Luzanía, RA and Ortega-Urquieta, ME and Aguilera-Ibarra, J and Morales-Sandoval, PH and Hernández-Coss, JA and González-Vázquez, LA and Jara-Morales, VB and Arredondo-Márquez, SH and Olea-Félix, MJ and de Los Santos-Villalobos, S}, title = {Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100289}, pmid = {39469049}, issn = {2666-5174}, abstract = {Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, emphasizing their genomic resources and their potential in the genomic mining of toxin-related genes.}, }
@article {pmid39467848, year = {2024}, author = {Büttiker, P and Boukherissa, A and Weissenberger, S and Ptacek, R and Anders, M and Raboch, J and Stefano, GB}, title = {Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.}, journal = {Cellular and molecular neurobiology}, volume = {44}, number = {1}, pages = {72}, pmid = {39467848}, issn = {1573-6830}, mesh = {Humans ; *Molecular Mimicry ; Computational Biology/methods ; Cognition/physiology ; Protein Binding ; Amino Acid Sequence ; Viral Proteins/metabolism/chemistry ; Models, Molecular ; }, abstract = {Neurotropic pathogens, notably, herpesviruses, have been associated with significant neuropsychiatric effects. As a group, these pathogens can exploit molecular mimicry mechanisms to manipulate the host central nervous system to their advantage. Here, we present a systematic computational approach that may ultimately be used to unravel protein-protein interactions and molecular mimicry processes that have not yet been solved experimentally. Toward this end, we validate this approach by replicating a set of pre-existing experimental findings that document the structural and functional similarities shared by the human cytomegalovirus-encoded UL144 glycoprotein and human tumor necrosis factor receptor superfamily member 14 (TNFRSF14). We began with a thorough exploration of the Homo sapiens protein database using the Basic Local Alignment Search Tool (BLASTx) to identify proteins sharing sequence homology with UL144. Subsequently, we used AlphaFold2 to predict the independent three-dimensional structures of UL144 and TNFRSF14. This was followed by a comprehensive structural comparison facilitated by Distance-Matrix Alignment and Foldseek. Finally, we used AlphaFold-multimer and PPIscreenML to elucidate potential protein complexes and confirm the predicted binding activities of both UL144 and TNFRSF14. We then used our in silico approach to replicate the experimental finding that revealed TNFRSF14 binding to both B- and T-lymphocyte attenuator (BTLA) and glycoprotein domain and UL144 binding to BTLA alone. This computational framework offers promise in identifying structural similarities and interactions between pathogen-encoded proteins and their host counterparts. This information will provide valuable insights into the cognitive mechanisms underlying the neuropsychiatric effects of viral infections.}, }
@article {pmid39466727, year = {2024}, author = {Charniga, K and Park, SW and Akhmetzhanov, AR and Cori, A and Dushoff, J and Funk, S and Gostic, KM and Linton, NM and Lison, A and Overton, CE and Pulliam, JRC and Ward, T and Cauchemez, S and Abbott, S}, title = {Best practices for estimating and reporting epidemiological delay distributions of infectious diseases.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012520}, pmid = {39466727}, issn = {1553-7358}, mesh = {Humans ; *Communicable Diseases/epidemiology ; *Disease Outbreaks/statistics & numerical data ; Models, Statistical ; Computational Biology/methods ; Epidemiological Models ; }, abstract = {Epidemiological delays are key quantities that inform public health policy and clinical practice. They are used as inputs for mathematical and statistical models, which in turn can guide control strategies. In recent work, we found that censoring, right truncation, and dynamical bias were rarely addressed correctly when estimating delays and that these biases were large enough to have knock-on impacts across a large number of use cases. Here, we formulate a checklist of best practices for estimating and reporting epidemiological delays. We also provide a flowchart to guide practitioners based on their data. Our examples are focused on the incubation period and serial interval due to their importance in outbreak response and modeling, but our recommendations are applicable to other delays. The recommendations, which are based on the literature and our experience estimating epidemiological delay distributions during outbreak responses, can help improve the robustness and utility of reported estimates and provide guidance for the evaluation of estimates for downstream use in transmission models or other analyses.}, }
@article {pmid39464503, year = {2023}, author = {Weir, JC and , and , and , and , and , and , and Boyes, D}, title = {The genome sequence of the Vapourer moth, Orgyia antiqua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {314}, pmid = {39464503}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Orgyia antiqua specimen (the Vapourer moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 480.1 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,475 protein coding genes.}, }
@article {pmid39464235, year = {2022}, author = {Boyes, D and , and , and , and , and , and Lewin, T and , }, title = {The genome sequence of the acorn piercer, Pammene fasciana (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {258}, pmid = {39464235}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Pammene fasciana (acorn piercer; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 564 megabases in span. Most of the assembly (99.94%) is scaffolded into 28 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,224 protein-coding genes.}, }
@article {pmid39461044, year = {2024}, author = {Wu, Y and Wei, C and Zhang, Y and Gu, C and Fang, Y}, title = {Investigating intrinsic and situational predictors of depression among older adults: An analysis of the CHARLS database.}, journal = {Asian journal of psychiatry}, volume = {102}, number = {}, pages = {104279}, doi = {10.1016/j.ajp.2024.104279}, pmid = {39461044}, issn = {1876-2026}, mesh = {Humans ; Female ; Male ; Aged ; Middle Aged ; Aged, 80 and over ; *Depression/epidemiology ; Databases, Factual ; China/epidemiology ; Risk Factors ; Follow-Up Studies ; Depressive Disorder/epidemiology ; Chronic Disease ; }, abstract = {BACKGROUND: This study aimed to investigate the intrinsic and situational predictors of depression under the health ecological model.
METHODS: Two waves (2011 and 2013) of survey data were collected from the CHARLS. A total of 5845 older adults (≧60) were included, and depression was defined as CESD-10 score ≧10. Random forest combined with interpretable methods were utilized to select important predictors of depression. Multilevel logit model was used to examine the associations of intrinsic and situational predictors with depression.
RESULTS: After a 2-year follow up, 1822 individuals (31.17 %) developed depression. Interpretable analyses showed that both intrinsic and situational variables were predictive for depression. Multilevel logit model showed that age, gender, number of chronic diseases, number of pain areas, life satisfaction, and toilet distance were significantly associated with depression.
CONCLUSION: Both intrinsic and situational factors were found to be associated with depression among community older population, highlighting their significance for early prevention from the perspective of public health.}, }
@article {pmid39460934, year = {2024}, author = {Frazer, SA and Baghbanzadeh, M and Rahnavard, A and Crandall, KA and Oakley, TH}, title = {Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD).}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39460934}, issn = {2047-217X}, support = {DEB-2153773//National Science Foundation/ ; }, mesh = {*Machine Learning ; *Opsins/genetics/metabolism ; Animals ; *Phenotype ; *Databases, Genetic ; Genetic Association Studies ; Genotype ; Humans ; Mutation ; }, abstract = {BACKGROUND: Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families, including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax-the wavelength of maximum absorbance-which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.
RESULTS: Here, we report a newly compiled database of all heterologously expressed opsin genes with λmax phenotypes that we call the Visual Physiology Opsin Database (VPOD). VPOD_1.0 contains 864 unique opsin genotypes and corresponding λmax phenotypes collected across all animals from 73 separate publications. We use VPOD data and deepBreaks to show regression-based machine learning (ML) models often reliably predict λmax, account for nonadditive effects of mutations on function, and identify functionally critical amino acid sites.
CONCLUSION: The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism's ecological niche, and may be used more broadly for de novo protein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.}, }
@article {pmid39460811, year = {2024}, author = {Hasan, A and Ibrahim, M and Alonazi, WB and Yu, R and Li, B}, title = {Pangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.}, journal = {Molecular genetics and genomics : MGG}, volume = {299}, number = {1}, pages = {101}, pmid = {39460811}, issn = {1617-4623}, mesh = {Humans ; *Tropheryma/genetics/immunology ; *Bacterial Vaccines/immunology/genetics ; Whipple Disease/immunology/microbiology/genetics ; Computational Biology/methods ; Bacterial Proteins/genetics/immunology ; Genome, Bacterial ; Epitopes/immunology/genetics ; Vaccine Development ; Immunodominant Epitopes/immunology/genetics ; Proteomics/methods ; Proteome/genetics/immunology ; }, abstract = {Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.}, }
@article {pmid39454020, year = {2024}, author = {Wong, R and Matulewicz, RS and Talwar, R and Shoenbill, KA and Goldstein, AO and Bjurlin, MA}, title = {Increased tobacco taxation associated with decreased consumption and bladder cancer incidence.}, journal = {Urology practice}, volume = {}, number = {}, pages = {101097UPJ0000000000000743}, doi = {10.1097/UPJ.0000000000000743}, pmid = {39454020}, issn = {2352-0787}, abstract = {PURPOSE: The temporal relationship between smoking exposure and bladder cancer (BC) diagnosis remains ill-defined. This study aims to cross-correlate and temporally associate changes in United States (US) tobacco tax and consumption with BC incidence.
METHODS: US tobacco consumption, tobacco tax data, and BC incidence rates from 1975-2019 were retrieved. A cross-correlation lag time for tobacco tax and consumption on BC incidence was calculated while controlling for national health expenditure. Proxied lag weighted semi-log linear models to determine the rate of change in BC incidence rates associated with a 1% change in tobacco tax percentages on a national and state level.
RESULTS: A 1% increase in tobacco tax was associated with a 1.77% decrease in BC incidence over a 6-year period (R[2]=0.9687, p=0.00044). 22 states had a statistically significant decline in BC incidences correlated with increasing tobacco taxation. Reduction in BC incidence >0.5% were observed in states along the Western and Eastern US borders. Montana, Utah, Nebraska, Arkansas, and Tennessee did not have decreasing BC incidences from tobacco tax increases. California had the most drastic decline in BC incidence (1.98%). Nationally, tobacco consumption decrease in 1 pack per capita was associated with a 0.47% decrease in BC incidence over a 28-year period (R[2]=0.984, p=0.00011).
CONCLUSION: Declining US tobacco consumption may indicate significant reduction in BC incidence through 2047. Primary prevention through adaptation of state-legislated tax changes may contribute to a reduction in BC incidence in states lying within the Central US. A national tobacco tax initative can be considered given the improvement in population health.}, }
@article {pmid39449983, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Currant Clearwing moth, Synanthedon tipuliformis (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {300}, pmid = {39449983}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Synanthedon tipuliformis (the Currant Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 295.8 megabases in span. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 27.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,878 protein-coding genes.}, }
@article {pmid39448189, year = {2024}, author = {Konečný, L and Peterková, K}, title = {Unveiling the peptidases of parasites from the office chair - The endothelin-converting enzyme case study.}, journal = {Advances in parasitology}, volume = {126}, number = {}, pages = {1-52}, doi = {10.1016/bs.apar.2024.05.003}, pmid = {39448189}, issn = {2163-6079}, mesh = {Animals ; *Computational Biology ; Endothelin-Converting Enzymes/genetics ; Schistosoma mansoni/enzymology/genetics ; Humans ; Peptide Hydrolases/genetics/metabolism ; Proteomics ; }, abstract = {The emergence of high-throughput methodologies such as next-generation sequencing and proteomics has necessitated significant advancements in biological databases and bioinformatic tools, therefore reshaping the landscape of research into parasitic peptidases. In this review we outline the development of these resources along the -omics technologies and their transformative impact on the field. Apart from extensive summary of general and specific databases and tools, we provide a general pipeline on how to use these resources effectively to identify candidate peptidases from these large datasets and how to gain as much information about them as possible without leaving the office chair. This pipeline is then applied in an illustrative case study on the endothelin-converting enzyme 1 homologue from Schistosoma mansoni and attempts to highlight the contemporary capabilities of bioinformatics. The case study demonstrate how such approach can aid to hypothesize enzyme functions and interactions through computational analysis alone effectively and emphasizes how such virtual investigations can guide and optimize subsequent wet lab experiments therefore potentially saving precious time and resources. Finally, by showing what can be achieved without traditional wet laboratory methods, this review provides a compelling narrative on the use of bioinformatics to bridge the gap between big data and practical research applications, highlighting the key role of these technologies in furthering our understanding of parasitic diseases.}, }
@article {pmid39446479, year = {2024}, author = {Oliveira, J and Aires Dias, J and Correia, R and Pinheiro, R and Reis, V and Sousa, D and Agostinho, D and Simões, M and Castelo-Branco, M}, title = {Exploring Immersive Multimodal Virtual Reality Training, Affective States, and Ecological Validity in Healthy Firefighters: Quasi-Experimental Study.}, journal = {JMIR serious games}, volume = {12}, number = {}, pages = {e53683}, pmid = {39446479}, issn = {2291-9279}, abstract = {BACKGROUND: Firefighters face stressful life-threatening events requiring fast decision-making. To better prepare for those situations, training is paramount, but errors in real-life training can be harmful. Virtual reality (VR) simulations provide the desired realism while enabling practice in a secure and controlled environment. Firefighters' affective states are also crucial as they are a higher-risk group.
OBJECTIVE: To assess the impact on affective states of 2 simulated immersive experiences in a sample of healthy firefighters (before, during, and after the simulation), we pursued a multivariate approach comprising cognitive performance, situational awareness, depression, anxiety, stress, number of previous adverse events experienced, posttraumatic stress disorder (PTSD) severity, and emotions. The efficacy and ecological validity of an innovative VR haptic system were also tested, exploring its impact on performance.
METHODS: In collaboration with the Portuguese National Fire Service School, we exposed 22 healthy firefighters to 2 immersive scenarios using the FLAIM Trainer VR system (neutral and arousing scenarios) while recording physiological data in a quasi-experimental study. Baseline cognitive performance, depression, anxiety, stress, number of adverse events, and severity of PTSD symptoms were evaluated. Positive and negative affective states were measured before, between, and after each scenario. Situational awareness, sense of presence, ecological validity, engagement, and negative effects resulting from VR immersion were tested.
RESULTS: Baseline positive affect score was high (mean 32.4, SD 7.2) and increased after the VR tasks (partial η[2]=0.52; Greenhouse-Geisser F1.82,32.78=19.73; P<.001). Contrarily, mean negative affect score remained low (range 11.0-11.9) throughout the study (partial η[2]=0.02; Greenhouse-Geisser F2.13,38.4=0.39; P=.69). Participants' feedback on the VR sense of presence was also positive, reporting a high sense of physical space (mean score 3.9, SD 0.8), ecological validity (mean score 3.8, SD 0.6), and engagement (mean score 3.8, SD 0.6). Engagement was related to the number of previously experienced adverse events (r=0.49; P=.02) and positive affect (after the last VR task; r=0.55; P=.02). Conversely, participants reported few negative effects (mean score 1.7, SD 0.6). The negative effects correlated positively with negative affect (after the last VR task; r=0.53; P=.03); and avoidance (r=0.73; P<.001), a PTSD symptom, controlling for relevant baseline variables. Performance related to situational awareness was positive (mean 46.4, SD 34.5), although no relation was found to metacognitively perceived situational awareness (r=-0.12; P=.59).
CONCLUSIONS: We show that VR is an effective alternative to in-person training as it was considered ecologically valid and engaging while promoting positive emotions, with few negative repercussions. This corroborates the use of VR to test firefighters' performance and situational awareness. Further research is needed to ascertain that firefighters with PTSD symptomatology are not negatively affected by VR. This study favors the use of VR training and provides new insights on its emotional and cognitive impact on the trainee.}, }
@article {pmid39445720, year = {2024}, author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM}, title = {Cancer Prevalence across Vertebrates.}, journal = {Cancer discovery}, volume = {}, number = {}, pages = {OF1-OF18}, doi = {10.1158/2159-8290.CD-24-0573}, pmid = {39445720}, issn = {2159-8290}, support = {P01 CA091955/CA/NCI NIH HHS/United States ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; U54 CA217376/CA/NCI NIH HHS/United States ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; U2C CA233254/CA/NCI NIH HHS/United States ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; R01 CA140657/CA/NCI NIH HHS/United States ; R21 CA257980/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; }, abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.}, }
@article {pmid39442119, year = {2024}, author = {Castro-Nunes, P and Palmieri, P and Bellas, H and Soares, A and Viana, J and Carvalho, PVR and Jatobá, A}, title = {Effects of pay for performance in primary care in an under-registration scenario.}, journal = {Revista de saude publica}, volume = {58}, number = {}, pages = {44}, pmid = {39442119}, issn = {1518-8787}, mesh = {Humans ; *Primary Health Care/economics ; Brazil ; *Reimbursement, Incentive/economics ; Female ; National Health Programs/economics ; }, abstract = {OBJECTIVE: To propose a method for detecting and analyzing under-registration and highlight its potential financial effect in view of the implementation of the Previne Brasil Program.
METHODS: An ecological study was carried out to analyze cytopathological exams in programmatic area 3.1 in the municipality of Rio de Janeiro. The data was collected from the Departamento de Informática do Sistema Único de Saúde (DATASUS - Department of Informatics of the Unified Health System) database, including information on reports from outsourced cytopathology laboratories and those available in the Sistema de Informação em Saúde para a Atenção Básica (SISAB - Health Information System for Primary Care) and the Sistema de Informação do Câncer do Colo do Útero (SISCOLO - Cervical Cancer Information System) of DATASUS/Ministry of Health.
RESULTS: The estimated under-registrations per health unit totaled 108,511 exams in the last two years in the programmatic area 3.1 area, which corresponds to an estimated total of R$ 435,129.00 that would have been foregone if the Previne Brasil Program had been in place during the period studied.
CONCLUSION: The article's main contribution lies in the presentation of empirical evidence of the potential effects of under-registration on Primary Health Care financing. In addition, there are two other significant findings - firstly, it highlights weaknesses in the process of recording health information inherent to vulnerable regions; secondly, it indicates a vicious circle potentially fueled by sudden changes in Primary Health Care funding conditions, in addition to potential consequences for other levels of care.}, }
@article {pmid39440963, year = {2024}, author = {Wang, Y and Sun, Y and Huang, K and Gao, Y and Lin, Y and Yuan, B and Wang, X and Xu, G and Nussio, LG and Yang, F and Ni, K}, title = {Multi-omics analysis reveals the core microbiome and biomarker for nutrition degradation in alfalfa silage fermentation.}, journal = {mSystems}, volume = {9}, number = {11}, pages = {e0068224}, pmid = {39440963}, issn = {2379-5077}, support = {32171686//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Medicago sativa/microbiology/metabolism ; *Silage/microbiology ; *Fermentation ; *Microbiota/genetics ; Animals ; Biomarkers/metabolism ; Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Cattle ; Multiomics ; }, abstract = {UNLABELLED: Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage crops globally, and its nutritional quality critically influences the productivity of dairy cows. Silage fermentation is recognized as a crucial technique for the preservation of fresh forage, ensuring the retention of its vital nutrients. However, the detailed microbial components and their functions in silage fermentation are not fully understood. This study integrated large-scale microbial culturing with high-throughput sequencing to thoroughly examine the microbial community structure in alfalfa silage and explored the potential pathways of nutritional degradation via metagenomic analysis. The findings revealed an enriched microbial diversity in silage, indicated by the identification of amplicon sequence variants. Significantly, the large-scale culturing approach recovered a considerable number of unique microbes undetectable by high-throughput sequencing. Predominant genera, such as Lactiplantibacillus, Leuconostoc, Lentilactobacillus, Weissella, and Liquorilactobacillus, were identified based on their abundance and prevalence. Additionally, genes associated with Enterobacteriaceae were discovered, which might be involved in pathways leading to the production of ammonia-N and butyric acid. Overall, this study offers a comprehensive insight into the microbial ecology of silage fermentation and provides valuable information for leveraging microbial consortia to enhance fermentation quality.
IMPORTANCE: Silage fermentation is a microbial-driven anaerobic process that efficiently converts various substrates into nutrients readily absorbable and metabolizable by ruminant animals. This study, integrating culturomics and metagenomics, has successfully identified core microorganisms involved in silage fermentation, including those at low abundance. This discovery is crucial for the targeted cultivation of specific microorganisms to optimize fermentation processes. Furthermore, our research has uncovered signature microorganisms that play pivotal roles in nutrient metabolism, significantly advancing our understanding of the intricate relationships between microbial communities and nutrient degradation during silage fermentation.}, }
@article {pmid39439296, year = {2025}, author = {Rosche, C and Broennimann, O and Novikov, A and Mrázová, V and Boiko, GV and Danihelka, J and Gastner, MT and Guisan, A and Kožić, K and Lehnert, M and Müller-Schärer, H and Nagy, DU and Remelgado, R and Ronikier, M and Selke, JA and Shiyan, NM and Suchan, T and Thoma, AE and Zdvořák, P and Mráz, P}, title = {Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe.}, journal = {The New phytologist}, volume = {245}, number = {1}, pages = {392-405}, pmid = {39439296}, issn = {1469-8137}, mesh = {*Centaurea/genetics/physiology ; Europe ; *Polyploidy ; *Introduced Species ; Phylogeography ; Ecosystem ; Diploidy ; }, abstract = {Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.}, }
@article {pmid39438357, year = {2024}, author = {Little, AJ and Matthee, CA and Ueckermann, EA and Horak, IG and Hui, C and Matthee, S}, title = {Host and habitat shape ectoparasite diversity on Mastomys natalensis and Mastomys coucha (Muridae).}, journal = {Parasitology}, volume = {151}, number = {8}, pages = {769-783}, pmid = {39438357}, issn = {1469-8161}, support = {R01 AI136832/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Rodent Diseases/parasitology/epidemiology ; *Ecosystem ; *Murinae/parasitology ; Male ; *Ectoparasitic Infestations/parasitology/veterinary ; Female ; Host-Parasite Interactions ; Mites/physiology/classification ; Siphonaptera/classification/physiology ; Biodiversity ; Ticks/classification/physiology ; }, abstract = {Mastomys natalensis and M. coucha are commensal rodent species endemic to Africa. A recent taxonomic revision within Mastomys leaves the parasite–host list of M. natalensis questionable and that of M. coucha incomplete. The current study aimed to develop a better understanding of the ectoparasite diversity associated with the 2 distinct but closely related rodent species and to explore the influence of host and habitat type on ectoparasite infestations. Between 2014 and 2020, 590 rodents were trapped in 3 habitat types (village, agriculture and natural) across a wildlife-human/domestic animal interface. In total 48 epifaunistic species (45 ectoparasitic and 3 predatory) represented by 29 genera from 4 taxonomic groups (fleas, lice, mites and ticks) were recorded. Only 50% of the epifauna were shared between the 2 rodent species, with mites the most speciose taxon in both host species. The abundance of epifaunistic individuals, and also those of mites and fleas, were significantly higher on male M. natalensis, while ticks were significantly higher on reproductively active M. natalensis. For both rodent species, infestations by most epifaunistic taxa (on M. natalensis) and some taxa (on M. coucha) were significantly lower in the village as opposed to the less disturbed agricultural and natural habitat types. The study highlights the importance of host life history, even in closely related rodent species, in shaping parasite profiles and a loss of parasite diversity in more extreme anthropogenic habitats.}, }
@article {pmid39436938, year = {2024}, author = {Rocha, U and Kasmanas, JC and Toscan, R and Sanches, DS and Magnusdottir, S and Saraiva, JP}, title = {Simulation of 69 microbial communities indicates sequencing depth and false positives are major drivers of bias in prokaryotic metagenome-assembled genome recovery.}, journal = {PLoS computational biology}, volume = {20}, number = {10}, pages = {e1012530}, pmid = {39436938}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; *Computer Simulation ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Bacteria/genetics/classification ; Genome, Bacterial/genetics ; }, abstract = {We hypothesize that sample species abundance, sequencing depth, and taxonomic relatedness influence the recovery of metagenome-assembled genomes (MAGs). To test this hypothesis, we assessed MAG recovery in three in silico microbial communities composed of 42 species with the same richness but different sample species abundance, sequencing depth, and taxonomic distribution profiles using three different pipelines for MAG recovery. The pipeline developed by Parks and colleagues (8K) generated the highest number of MAGs and the lowest number of true positives per community profile. The pipeline by Karst and colleagues (DT) showed the most accurate results (~ 92%), outperforming the 8K and Multi-Metagenome pipeline (MM) developed by Albertsen and collaborators. Sequencing depth influenced the accurate recovery of genomes when using the 8K and MM, even with contrasting patterns: the MM pipeline recovered more MAGs found in the original communities when employing sequencing depths up to 60 million reads, while the 8K recovered more true positives in communities sequenced above 60 million reads. DT showed the best species recovery from the same genus, even though close-related species have a low recovery rate in all pipelines. Our results highlight that more bins do not translate to the actual community composition and that sequencing depth plays a role in MAG recovery and increased community resolution. Even low MAG recovery error rates can significantly impact biological inferences. Our data indicates that the scientific community should curate their findings from MAG recovery, especially when asserting novel species or metabolic traits.}, }
@article {pmid39436510, year = {2024}, author = {Zinicovscaia, I and Chernyagina, O and Chaligava, O and Yushin, N and Devyatova, E and Grozov, D}, title = {Moss biomonitoring in areas affected by ashfalls of Shiveluch volcano (Kamchatka).}, journal = {Environmental science and pollution research international}, volume = {31}, number = {52}, pages = {61730-61739}, pmid = {39436510}, issn = {1614-7499}, mesh = {*Bryophyta/chemistry ; *Volcanic Eruptions ; *Environmental Monitoring/methods ; *Biological Monitoring ; Air Pollutants/analysis ; }, abstract = {The moss bag technique was applied on Kamchatka to assess the effect of Shiveluch volcano on the air quality. Moss bags were exposed in settlements located at different distances from the volcano and affected by ashfall to varying degrees. The inductively coupled plasma optical emission spectrometry was used for the determination of the content of Al, Ba, Co, Cd, Cr, Cu, Fe, Mn, P, Pb, Sr, S, V, and Zn in both exposed and unexposed moss samples. Relative accumulation factor revealed enrichment of mosses exposed in the area affected by ashfall with Al, Cr, V, and Zn. Correlation and principal component analysis allowed to identify elements of volcanogenic, geogenic, and anthropogenic origin. Ecological risk values less than 150 indicate low potential ecological risk in the region. Active moss biomonitoring can be considered a cheap and efficient tool for in-depth study of the influence of volcanic activity on air quality on the peninsula.}, }
@article {pmid39435526, year = {2025}, author = {Kan-Lingwood, NY and Sagi, L and Mazie, S and Shahar, N and Zecherle Bitton, L and Templeton, A and Rubenstein, D and Bouskila, A and Bar-David, S}, title = {Genotyping Error Detection and Customised Filtration for SNP Datasets.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14033}, doi = {10.1111/1755-0998.14033}, pmid = {39435526}, issn = {1755-0998}, support = {2011384//United States-Israel Binational Science Foundation/ ; }, mesh = {*Polymorphism, Single Nucleotide ; *Genotyping Techniques/methods ; Animals ; Genotype ; Computational Biology/methods ; }, abstract = {A major challenge in analysing single-nucleotide polymorphism (SNP) genotype datasets is detecting and filtering errors that bias analyses and misinterpret ecological and evolutionary processes. Here, we present a comprehensive method to estimate and minimise genotyping error rates (deviations from the 'true' genotype) in any SNP datasets using triplicates (three repeats of the same sample) in a four-step filtration pipeline. The approach involves: (1) SNP filtering by missing data; (2) SNP filtering by error rates; (3) sample filtering by missing data and (4) detection of recaptured individuals by using estimated SNP error rates. The modular pipeline is provided in an R script that allows customised adjustments. We demonstrate the applicability of the method using non-invasive sampling from the Asiatic wild ass (Equus hemionus) population in Israel. We genotyped 756 samples using 625 SNPs, of which 255 were triplicates of 85 samples. The average SNP error rate, calculated based on the number of mismatching genotypes across triplicates before filtration, was 0.0034 and was reduced to 0.00174 following filtration. Evaluating genetic distance (GD) and relatedness (r) between triplicates before and after filtration (expected to be at the minimum and maximum respectively) showed a significant reduction in the average GD, from 58.1 to 25.3 (p = 0.0002) and a significant increase in relatedness, from r = 0.98 to r = 0.991 (p = 0.00587). We demonstrate how error rate estimation enhances recapture detection and improves genotype quality.}, }
@article {pmid39434036, year = {2024}, author = {Li, C and Zhang, X and Zhao, L and Liu, S}, title = {Multi-omics profiling reveals the molecular mechanisms of H2O2-induced detrimental effects on Thamnaconus septentrionalis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {984}, pmid = {39434036}, issn = {1471-2164}, mesh = {Animals ; *Hydrogen Peroxide/metabolism ; Fishes/metabolism/genetics ; Transcriptome/drug effects ; Gene Expression Profiling ; Metabolomics ; Signal Transduction/drug effects ; Metabolome/drug effects ; Multiomics ; }, abstract = {BACKGROUND: Hydrogen peroxide (H2O2), a novel water treatment agent, can be used for disinfection, water quality adjustment, and disease prevention, while excessive H2O2 can injure farm animals, even leading to death. Hydrogen peroxide is a recommended disinfectant and bactericide for treating gill diseases and vibriosis in the greenfin horse-faced filefish Thamnaconus septentrionalis. However, its cumulative effect, toxic molecular mechanism and relevant signal transduction/metabolic networks in marine fishes are largely unknown.
RESULTS: We employed a multi-omics approach to investigate the detrimental effects of 50 mg/L H2O2 exposure (2 h/d) on filefish for 2 d, 4 d, and 6 d. Transcriptome sequencing showed that differentially expressed genes (DEGs) were mainly classified into functions such as signal transduction, nervous system, liver and bile acid metabolism, energy metabolism, cell adhesion and communication, inflammation and immune response. Metabolomic analysis found that the significantly changed metabolites (SCMs) were involved in phenylalanine metabolism, inflammatory mediator regulation, linoleic acid metabolism, and necroptosis. The main SCMs were cholic acid, carnitine C12:1, dimethylmalonic acid, glutamic acid, L-lactic acid, shikimic acid, 2-methylsuccinic acid, and others. Moreover, H2O2-induced oxidative stress also disturbs the balance of the gut microbiota, altering the microbial composition and affecting digestive processes.
CONCLUSIONS: Integrated multiomics analysis revealed that H2O2-induced detrimental impacts include mucosal damage, inflammatory and immune responses, altered energy metabolism, and gut microbiota disorders. These findings offer novel insights into the harmful effects and signal transduction/metabolic pathways triggered by H2O2 exposure in marine fishes.}, }
@article {pmid39432055, year = {2025}, author = {Zhao, L and Henriksen, RA and Ramsøe, A and Nielsen, R and Korneliussen, TS}, title = {Revisiting the Briggs Ancient DNA Damage Model: A Fast Maximum Likelihood Method to Estimate Post-Mortem Damage.}, journal = {Molecular ecology resources}, volume = {25}, number = {1}, pages = {e14029}, pmid = {39432055}, issn = {1755-0998}, support = {CF19-0712//Carlsberg Foundation/ ; CF20-0071//Carlsberg Foundation/ ; R302-2018-2155//Lundbeck Foundation/ ; }, mesh = {*DNA, Ancient/analysis ; DNA Damage ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Humans ; }, abstract = {One essential initial step in the analysis of ancient DNA is to authenticate that the DNA sequencing reads are actually from ancient DNA. This is done by assessing if the reads exhibit typical characteristics of post-mortem damage (PMD), including cytosine deamination and nicks. We present a novel statistical method implemented in a fast multithreaded programme, ngsBriggs that enables rapid quantification of PMD by estimation of the Briggs ancient damage model parameters (Briggs parameters). Using a multinomial model with maximum likelihood fit, ngsBriggs accurately estimates the parameters of the Briggs model, quantifying the PMD signal from single and double-stranded DNA regions. We extend the original Briggs model to capture PMD signals for contemporary sequencing platforms and show that ngsBriggs accurately estimates the Briggs parameters across a variety of contamination levels. Classification of reads into ancient or modern reads, for the purpose of decontamination, is significantly more accurate using ngsBriggs than using other methods available. Furthermore, ngsBriggs is substantially faster than other state-of-the-art methods. ngsBriggs offers a practical and accurate method for researchers seeking to authenticate ancient DNA and improve the quality of their data.}, }
@article {pmid39430511, year = {2024}, author = {Shamrat, FMJM and Idna Idris, MY and Zhou, X and Khalid, M and Sharmin, S and Sharmin, Z and Ahmed, K and Moni, MA}, title = {PollenNet: A novel architecture for high precision pollen grain classification through deep learning and explainable AI.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38596}, pmid = {39430511}, issn = {2405-8440}, abstract = {Pollen grains play a critical role in environmental, agricultural, and allergy research despite their tiny dimensions. The accurate classification of pollen grains remains a significant challenge, mainly attributable to their intricate structures and the extensive diversity of species. Traditional methods often lack accuracy and effectiveness, prompting the need for advanced solutions. This study introduces a novel deep learning framework, PollenNet, designed to tackle the intricate challenge of pollen grain image classification. The efficiency of PollenNet is thoroughly evaluated through stratified 5-fold cross-validation, comparing it with cutting-edge methods to demonstrate its superior performance. A comprehensive data preparation phase is conducted, including removing duplicates and low-quality images, applying Non-local Means Denoising for noise reduction, and Gamma correction to adjust image brightness. Furthermore, Explainable AI (XAI) is utilized to enhance the interpretability of the model, while Receiver Operating Characteristic (ROC) curve analysis serves as a quantitative method for evaluating the model's capabilities. PollenNet demonstrates superior performance when compared to existing models, with an accuracy of 98.45 %, precision of 98.20 %, specificity of 98.40 %, recall of 98.30 %, and f1-score of 98.25 %. The model also maintains low Mean Squared Error (0.03) and Mean Absolute Error (0.02) rates. The ROC curve analysis, the low False Positive Rate (0.016), and the False Negative Rate (0.017) highlight the reliability and dependability of the model. This study significantly improves the efficacy of classifying pollen grains, indicating an important advancement in the application of deep learning for ecological research.}, }
@article {pmid39429633, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Hebrew Character, Orthosia gothica (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {90}, pmid = {39429633}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Orthosia gothica (the Hebrew character; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 1,065.1 megabases in span. Most of the assembly is scaffolded into 37 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,691 protein coding genes.}, }
@article {pmid39429632, year = {2024}, author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of the smooth giant clam, Tridacna derasa Röding, 1798.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {375}, pmid = {39429632}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Tridacna derasa (the smooth giant clam; Mollusca; Bivalvia;Cardiida; Cardiidae). The genome sequence is 1,060.2 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.95 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,638 protein coding genes.}, }
@article {pmid39424895, year = {2024}, author = {Melo, MS and Lima, SVMA and Dos Santos, AD and Ribeiro, CJN and Júnior, PAB and Silva, TKS and de Resende, LT and Corrêa, F and Migowski, A and Schiffman, M and Rodriguez, AC and Ribeiro, A and Raiol, T}, title = {Temporal trends, spatial and spatiotemporal clusters of cervical cancer mortality in Brazil from 2000 to 2021.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24436}, pmid = {39424895}, issn = {2045-2322}, support = {Grant number GEREB-Fiocruz/CNPq 440204/2019-4.//Oswaldo Cruz Foundation (Fiocruz) and National Council for Scientific and Technological Development (CNPq)/ ; }, mesh = {Humans ; Female ; Brazil/epidemiology ; *Uterine Cervical Neoplasms/mortality/epidemiology ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Aged ; Young Adult ; Adolescent ; Mortality/trends ; }, abstract = {Cervical cancer, despite being preventable through primary and secondary prevention strategies, remains one of the leading causes of morbidity and mortality among women in Brazil. This study aimed to analyze the temporal, spatial, and space-time patterns of cervical cancer mortality in Brazil. An ecological study was conducted using temporal, spatial, and space-time analysis techniques, using death certificates with cervical cancer as the underlying cause or associated condition among females in Brazil from 2000 to 2021. Death certificate and population data were provided by the Department of Health Informatics of the Unified Health System (DATASUS) and the Brazilian Institute of Geography and Statistics (IBGE), respectively. A total of 123,306 deaths associated with cervical cancer among women were registered during the study period. A rising trend in mortality was detected since 2014 onwards, after 14 years of decline. Particularly, an increase in mortality was observed among the younger age groups, and in the North and Northeast regions regardless of age. Heterogeneity in the spatial distribution of cervical cancer mortality was observed, with high mortality clusters around the country, but mostly concentrated in the North and Northeast regions. These findings suggest a need and an opportunity to develop efficient and effective health policies targeting those regions and groups of women at higher risk which in turn will allow for fast and significant reductions in cervical cancer mortality in Brazil.}, }
@article {pmid39421415, year = {2024}, author = {Ion, MC and Bloomer, CC and Bărăscu, TI and Oficialdegui, FJ and Shoobs, NF and Williams, BW and Scheers, K and Clavero, M and Grandjean, F and Collas, M and Baudry, T and Loughman, Z and Wright, JJ and Ruokonen, TJ and Chucholl, C and Guareschi, S and Koese, B and Banyai, ZM and Hodson, J and Hurt, M and Kaldre, K and Lipták, B and Fetzner, JW and Cancellario, T and Weiperth, A and Birzaks, J and Trichkova, T and Todorov, M and Balalaikins, M and Griffin, B and Petko, ON and Acevedo-Alonso, A and D'Elía, G and Śliwińska, K and Alekhnovich, A and Choong, H and South, J and Whiterod, N and Zorić, K and Haase, P and Soto, I and Brady, DJ and Haubrock, PJ and Torres, PJ and Şadrin, D and Vlach, P and Kaya, C and Woo Jung, S and Kim, JY and Vermeersch, XHC and Bonk, M and Guiaşu, R and Harlioğlu, MM and Devlin, J and Kurtul, I and Błońska, D and Boets, P and Masigol, H and Cabe, PR and Jussila, J and Vrålstad, T and Beresford, DV and Reid, SM and Patoka, J and Strand, DA and Tarkan, AS and Steen, F and Abeel, T and Harwood, M and Auer, S and Kelly, S and Giantsis, IA and Maciaszek, R and Alvanou, MV and Aksu, Ö and Hayes, DM and Kawai, T and Tricarico, E and Chakandinakira, A and Barnett, ZC and Kudor, ŞG and Beda, AE and Vîlcea, L and Mizeranschi, AE and Neagul, M and Licz, A and Cotoarbă, AD and Petrusek, A and Kouba, A and Taylor, CA and Pârvulescu, L}, title = {World of Crayfish™: a web platform towards real-time global mapping of freshwater crayfish and their pathogens.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18229}, pmid = {39421415}, issn = {2167-8359}, mesh = {Animals ; *Astacoidea/microbiology ; *Fresh Water ; Aphanomyces ; Internet ; Ecosystem ; Databases, Factual ; }, abstract = {Freshwater crayfish are amongst the largest macroinvertebrates and play a keystone role in the ecosystems they occupy. Understanding the global distribution of these animals is often hindered due to a paucity of distributional data. Additionally, non-native crayfish introductions are becoming more frequent, which can cause severe environmental and economic impacts. Management decisions related to crayfish and their habitats require accurate, up-to-date distribution data and mapping tools. Such data are currently patchily distributed with limited accessibility and are rarely up-to-date. To address these challenges, we developed a versatile e-portal to host distributional data of freshwater crayfish and their pathogens (using Aphanomyces astaci, the causative agent of the crayfish plague, as the most prominent example). Populated with expert data and operating in near real-time, World of Crayfish™ is a living, publicly available database providing worldwide distributional data sourced by experts in the field. The database offers open access to the data through specialized standard geospatial services (Web Map Service, Web Feature Service) enabling users to view, embed, and download customizable outputs for various applications. The platform is designed to support technical enhancements in the future, with the potential to eventually incorporate various additional features. This tool serves as a step forward towards a modern era of conservation planning and management of freshwater biodiversity.}, }
@article {pmid39420601, year = {2024}, author = {Li, Z and Zhang, Y and Peng, B and Qin, S and Zhang, Q and Chen, Y and Chen, C and Bao, Y and Zhu, Y and Hong, Y and Liu, B and Liu, Q and Xu, L and Chen, X and Ma, X and Wang, H and Xie, L and Yao, Y and Deng, B and Li, J and De, B and Chen, Y and Wang, J and Li, T and Liu, R and Tang, Z and Cao, J and Zuo, E and Mei, C and Zhu, F and Shao, C and Wang, G and Sun, T and Wang, N and Liu, G and Ni, JQ and Liu, Y}, title = {A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.}, journal = {Nucleic acids research}, volume = {52}, number = {21}, pages = {13447-13468}, pmid = {39420601}, issn = {1362-4962}, support = {2021YFF1200500//China National Key R&D Program/ ; 32070595//National Natural Science Foundation of China/ ; 20221250020//Ministry of Science and Technology/ ; 20181300988//National Natural Science Foundation of China/ ; }, mesh = {*Enhancer Elements, Genetic ; Animals ; *Deep Learning ; Drosophila melanogaster/genetics ; Drosophila/genetics ; Humans ; Computational Biology/methods ; Gene Expression Regulation ; }, abstract = {Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design. Proficient in uncovering subtle and intricate patterns within extensive enhancer screening data, DREAM achieves cutting-edge sequence-based enhancer activity prediction and highlights critical sequence features implicating strong enhancer activity. Leveraging DREAM, we have engineered enhancers that surpass the potency of the strongest enhancer within the Drosophila genome by approximately 3.6-fold. Remarkably, these synthetic enhancers exhibited conserved functionality across species that have diverged more than billion years, indicating that DREAM was able to learn highly conserved enhancer regulatory grammar. Additionally, we designed silencers and cell line-specific enhancers using DREAM, demonstrating its versatility. Overall, our study not only introduces an interpretable approach for enhancer design but also lays out a general framework applicable to the design of other types of cis-regulatory elements.}, }
@article {pmid39419226, year = {2024}, author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z}, title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.}, journal = {The Science of the total environment}, volume = {955}, number = {}, pages = {176892}, doi = {10.1016/j.scitotenv.2024.176892}, pmid = {39419226}, issn = {1879-1026}, mesh = {*Nitrogen ; *Soil Microbiology ; *Microbiota/drug effects ; *Herbivory ; Animals ; *Insecta/physiology ; Desert Climate ; Soil/chemistry ; Biodiversity ; Grassland ; Ecosystem ; China ; }, abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.}, }
@article {pmid39417898, year = {2024}, author = {Khalaf, SMH and Alqahtani, MSM and Ali, MRM and Abdelalim, ITI and Hodhod, MS}, title = {Modeling climate-related global risk maps of rice bacterial blight caused by Xanthomonas oryzae (Ishiyama 1922) using geographical information system (GIS).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1064}, pmid = {39417898}, issn = {1573-2959}, mesh = {*Xanthomonas ; *Oryza/microbiology ; *Climate Change ; *Plant Diseases/microbiology/statistics & numerical data ; *Geographic Information Systems ; Environmental Monitoring ; Climate ; }, abstract = {Rice is a critical staple crop that feeds more than half of the world's population. Still, its production confronts various biotic risks, notably the severe bacterial blight disease produced by Xanthomonas oryzae. Understanding the possible effects of climate change on the geographic distribution of this virus is critical to ensuring food security. This work used ecological niche modeling and the Maxent algorithm to create future risk maps for the range of X. oryzae under several climate change scenarios between 2050 and 2070. The model was trained using 93 occurrence records of X. oryzae and five critical bioclimatic variables. It has an excellent predictive performance, with an AUC of 0.889. The results show that X. oryzae's potential geographic range and habitat suitability are expected to increase significantly under low (RCP2.6) and high (RCP8.5) emission scenarios. Key climatic drivers allowing this development include increased yearly precipitation, precipitation during the wettest quarter, and the wettest quarter's mean temperature. These findings are consistent with broader research revealing that climate change is allowing many plant diseases and other dangerous microbes to spread across the globe. Integrating these spatial predictions with data on host susceptibility, agricultural practices, and socioeconomic vulnerabilities can help to improve targeted surveillance, preventative, and management methods for reducing the growing threat of bacterial blight to rice production. Proactive, multidisciplinary efforts to manage the changing disease dynamics caused by climate change will be critical to assuring global food security in the future decades.}, }
@article {pmid39417330, year = {2024}, author = {Kershenbaum, A and Akçay, Ç and Babu-Saheer, L and Barnhill, A and Best, P and Cauzinille, J and Clink, D and Dassow, A and Dufourq, E and Growcott, J and Markham, A and Marti-Domken, B and Marxer, R and Muir, J and Reynolds, S and Root-Gutteridge, H and Sadhukhan, S and Schindler, L and Smith, BR and Stowell, D and Wascher, CAF and Dunn, JC}, title = {Automatic detection for bioacoustic research: a practical guide from and for biologists and computer scientists.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.13155}, pmid = {39417330}, issn = {1469-185X}, support = {//A*MIDEX/ ; //Cambridge Centre for Data-Driven Discovery/ ; //African Institute for Mathematical Sciences/ ; NE/W005468/1//Natural Environment Research Council/ ; //Global Affairs Canada/ ; ANR-20-CE23-0012-01 MIM//Agence Nationale de la Recherche/ ; ANR-20-CHIA-0014//Agence Nationale de la Recherche/ ; ANR-16-CONV-0002//Institute of Convergence ILCB/ ; //International Development Research Centre/ ; }, abstract = {Recent years have seen a dramatic rise in the use of passive acoustic monitoring (PAM) for biological and ecological applications, and a corresponding increase in the volume of data generated. However, data sets are often becoming so sizable that analysing them manually is increasingly burdensome and unrealistic. Fortunately, we have also seen a corresponding rise in computing power and the capability of machine learning algorithms, which offer the possibility of performing some of the analysis required for PAM automatically. Nonetheless, the field of automatic detection of acoustic events is still in its infancy in biology and ecology. In this review, we examine the trends in bioacoustic PAM applications, and their implications for the burgeoning amount of data that needs to be analysed. We explore the different methods of machine learning and other tools for scanning, analysing, and extracting acoustic events automatically from large volumes of recordings. We then provide a step-by-step practical guide for using automatic detection in bioacoustics. One of the biggest challenges for the greater use of automatic detection in bioacoustics is that there is often a gulf in expertise between the biological sciences and the field of machine learning and computer science. Therefore, this review first presents an overview of the requirements for automatic detection in bioacoustics, intended to familiarise those from a computer science background with the needs of the bioacoustics community, followed by an introduction to the key elements of machine learning and artificial intelligence that a biologist needs to understand to incorporate automatic detection into their research. We then provide a practical guide to building an automatic detection pipeline for bioacoustic data, and conclude with a discussion of possible future directions in this field.}, }
@article {pmid39415784, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and Laetsch, DR and Harnqvist, S and , and , and , and , and , }, title = {The genome sequence of the Essex Skipper butterfly, Thymelicus lineola (Ochsenheimer, 1808).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {452}, pmid = {39415784}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Essex Skipper butterfly, Thymelicus lineola (Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence spans 511.80 megabases. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.24 kilobases in length.}, }
@article {pmid39414803, year = {2024}, author = {Lončarević, N and Liu, U and Stefanaki, A and Carapeto, A and Ensslin, A and Meade, C and Metzing, D and Peci, D and Fantinato, E and Colling, G and Pankova, H and Akmane, I and Tsvetkov, IN and Sibik, J and Szitár, K and Van Meerbeek, K and Daco, L and Boudagher, M and Klisz, M and Walczak, M and Evju, M and Lužnik, M and Kiehn, M and Sarginci, M and Aksoy, N and Koçer, N and Barazani, O and Anastasiu, P and Stroh, P and Vit, P and Vergeer, P and Puchałka, R and Kahale, R and Godefroid, S and Lanfranco, S and Parpan, T and Kull, T and Rašomavičius, V and Fišer, Ž and Glasnović, P}, title = {Database of European vascular plants red lists as a contribution to more coherent plant conservation.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1138}, pmid = {39414803}, issn = {2052-4463}, support = {R25 CA018201/CA/NCI NIH HHS/United States ; CA18201//European Cooperation in Science and Technology (COST)/ ; }, mesh = {Europe ; *Databases, Factual ; *Conservation of Natural Resources ; *Plants/classification ; Biodiversity ; }, abstract = {We introduce the database of European vascular plant red lists, a compilation of red list categories designated to taxa during in-country conservation assessments. Version 1.0 of the database is a standalone static dataset with open access in an end-user friendly format. Its aim is to fulfil the objectives of European Cooperation in Science and Technology (COST) Action 18201, ConservePlants. The database synthesizes data across 42 red lists from 41 countries, with participation of 39 out of a total of 44 European countries and two additional Mediterranean countries. The database contains 51,109 records representing 21,481 original taxonomic names with 37 different red list categories. During data harmonisation, 20,312 of the original taxonomic names were assigned to 17,873 unique accepted taxonomic names with scientific authorships across 184 families, 1650 genera and 15,593 species; and red list categories were standardised to 13 unique categories. We see this database as a source of information in diverse plant conservation activities and suitable for various stakeholders.}, }
@article {pmid39409485, year = {2024}, author = {Jechow, A and Bumberger, J and Palm, B and Remmler, P and Schreck, G and Ogashawara, I and Kiel, C and Kohnert, K and Grossart, HP and Singer, GA and Nejstgaard, JC and Wollrab, S and Berger, SA and Hölker, F}, title = {Characterizing and Implementing the Hamamatsu C12880MA Mini-Spectrometer for Near-Surface Reflectance Measurements of Inland Waters.}, journal = {Sensors (Basel, Switzerland)}, volume = {24}, number = {19}, pages = {}, pmid = {39409485}, issn = {1424-8220}, support = {Leibniz Competition No. K45/2017 (CONNECT-Connectivity and synchronization of lake ecosystems in space and time)//Leibniz Association/ ; IGB Frontiers project (2017)//Leibniz Institute of Freshwater Ecology and Inland Fisheries/ ; }, abstract = {In recent decades, inland water remote sensing has seen growing interest and very strong development. This includes improved spatial resolution, increased revisiting times, advanced multispectral sensors and recently even hyperspectral sensors. However, inland waters are more challenging than oceanic waters due to their higher complexity of optically active constituents and stronger adjacency effects due to their small size and nearby vegetation and built structures. Thus, bio-optical modeling of inland waters requires higher ground-truthing efforts. Large-scale ground-based sensor networks that are robust, self-sufficient, non-maintenance-intensive and low-cost could assist this otherwise labor-intensive task. Furthermore, most existing sensor systems are rather expensive, precluding their employability. Recently, low-cost mini-spectrometers have become widely available, which could potentially solve this issue. In this study, we analyze the characteristics of such a mini-spectrometer, the Hamamatsu C12880MA, and test it regarding its application in measuring water-leaving radiance near the surface. Overall, the measurements performed in the laboratory and in the field show that the system is very suitable for the targeted application.}, }
@article {pmid39407030, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {31}, doi = {10.1038/s44185-024-00065-3}, pmid = {39407030}, issn = {2731-4243}, }
@article {pmid39404811, year = {2024}, author = {Litavský, J and Majzlan, O and Langraf, V and Žarnovičan, H}, title = {Influence of habitat management and selected environmental parameters on the ground-living communities of harvestmen (Opiliones) in the historical park in Rusovce (Slovakia).}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1056}, pmid = {39404811}, issn = {1573-2959}, support = {No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0007/21//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; No. 1/0255/23//Slovak Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic/ ; }, mesh = {*Ecosystem ; *Parks, Recreational ; *Environmental Monitoring ; Animals ; Slovakia ; Biodiversity ; Arachnida ; Conservation of Natural Resources/methods ; Forests ; Microclimate ; }, abstract = {City parks serve as valuable refuges for invertebrates in the urban environment, which are constantly exposed to human influence caused by management practices in the parks. Many harvestman species are suitable bioindicators for monitoring ecological change; however, their effective use in environmental assessment necessitates to expand the insufficient knowledge of ecological environmental specificities of their communities. We studied the diversity and dynamics of harvestman (Opiliones) communities in the historical park in Rusovce, situated in the southwestern part of Bratislava (Slovakia). Seven study sites were investigated, representing areas subjected to different management practices. The research was conducted from March 2019 to April 2020, using pitfall traps. We evaluated the impact of microclimatic variables (soil and air temperature), environmental characteristics (plant diversity and cover of vegetation layers, age of forest stands, thickness of the litter layer), and management practices on the structure of harvestman communities. The study revealed the response of specific harvestman species to temperature variations, emphasizing the importance of microclimatic conditions. Environmental variables, such as the richness of plant species in the shrub layer, the cover of the herb and shrub vegetation layers, and the age of the forest stands, were identified as key factors that influence the dispersal of harvestman species. Furthermore, management practices, especially the presence of monoculture tree plantations, significantly affected the species composition of harvestmen. Examining the sensitivity of Opiliones, important bioindicators, to these factors is crucial for implementing effective conservation strategies in urban green spaces and anthropogenically influenced ecosystems.}, }
@article {pmid39403498, year = {2024}, author = {Hung, RJ and Low, I and Yeh, HC and Wang, PY and Chen, YS and Chen, LF}, title = {Feedback matters: EEG correlates of empathy involved in the naturalistic communication of emotions.}, journal = {Heliyon}, volume = {10}, number = {19}, pages = {e38574}, pmid = {39403498}, issn = {2405-8440}, abstract = {Empathy involves the processing of complex information related to dynamic interactions between the empathizer and target. One neural signature of empathy is the suppression of electroencephalographic mu rhythm (8-13 Hz) over the sensorimotor region. It is important to consider that few researchers have studied the effects of empathizer feedback on empathy and its underlying neural mechanism, and most previous research has lacked ecological validity due to standardized emotional stimuli and constraints on the experiment environment. Our objective in this study was to investigate the means by which empathizer feedback influences one's own empathy in naturalistic social situations. Our results revealed that empathizer feedback decreases empathic accuracy but does not affect the emotional contagion nor the emotional intensity of the empathizer. We also found that the ability to accurately infer sadness is hindered by empathizer feedback. Empathizers presented lower alpha activity in the sensorimotor cortical areas only while receiving sad narratives and not providing feedback. This study contributes to the emerging research on the influence of empathizer feedback in naturalistic social settings.}, }
@article {pmid39403309, year = {2024}, author = {Sivell, O and Sivell, D and Webb, JA and Mitchell, R and Ashworth, M and , and , and , and , and , and , and , }, title = {The genome sequence of the acalyptrate fly Dryomyza anilis Fallén, 1820.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {440}, pmid = {39403309}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male acalyptrate fly Dryomyza anilis (Arthropoda; Insecta; Diptera; Dryomyzidae). The genome sequence has a total length of 656.60 megabases. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.48 kilobases in length.}, }
@article {pmid39401552, year = {2024}, author = {Yan, X and Zhao, Z and Feng, S and Zhang, Y and Wang, Z and Li, Z}, title = {Multi-omics analysis reveal the fall armyworm Spodoptera frugiperda tolerate high temperature by mediating chitin-related genes.}, journal = {Insect biochemistry and molecular biology}, volume = {174}, number = {}, pages = {104192}, doi = {10.1016/j.ibmb.2024.104192}, pmid = {39401552}, issn = {1879-0240}, mesh = {Animals ; *Spodoptera/genetics/growth & development/metabolism/physiology ; *Chitin/metabolism ; Hot Temperature ; Larva/genetics/growth & development/metabolism ; CRISPR-Cas Systems ; Insect Proteins/metabolism/genetics ; Thermotolerance ; Transcriptome ; RNA Interference ; Multiomics ; }, abstract = {Climate change facilitates the rapid invasion of agricultural pests, threatening global food security. The fall armyworm Spodoptera frugiperda is a highly polyphagous migratory pest tolerant to high temperatures, allowing its proliferation in harsh thermal environments. We aimed to demonstrate mechanisms of its high-temperature tolerance, particularly transcriptional and metabolic regulation, which are poorly understood. To achieve the aim, we examined the impact and mechanism of heat events on S. frugiperda by using multiple approaches: ecological measurements, transcriptomics, metabolomics, RNAi, and CRISPR/Cas9 technology. We observed that several physiological indices (larval survival rate, larval period, pupation rate, pupal weight, eclosion rate, and average fecundity) decreased as the temperature increased, with the 32 °C treatment displaying a significant difference from the control group at 26 °C. Significantly upregulated expression of genes encoding endochitinase and chitin deacetylase was observed in the chitin-binding, extracellular region, and carbohydrate metabolic process GO terms of hemolymph, fat body, and brain, exhibiting a tissue-specific pattern. Significantly enriched pathways (e.g., cutin, suberin, and wax biosynthesis; oxidative phosphorylation and cofactor biosynthesis; diverse amino acid biosynthesis and degradation; carbon metabolism; and energy metabolism), all of which are essential for S. frugiperda larvae to tolerate temperature, were found in metabolites that were expressed differently. Successful RNA interference targeting of the three chitin-related genes reduced gene expression levels and larval survival rate. Knockout of the endochitinase gene by using the CRISPR/Cas9 system significantly reduced the relative gene expression and increased sensitivity to high-temperature exposure. On the basis of our findings, theoretical foundations for understanding the high-temperature tolerance of S. frugiperda populations and latent genetic control strategies were established.}, }
@article {pmid39401366, year = {2024}, author = {Posch, BC and Bush, SE and Koepke, DF and Schuessler, A and Anderegg, LLD and Aparecido, LMT and Blonder, BW and Guo, JS and Kerr, KL and Moran, ME and Cooper, HF and Doughty, CE and Gehring, CA and Whitham, TG and Allan, GJ and Hultine, KR}, title = {Intensive leaf cooling promotes tree survival during a record heatwave.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {43}, pages = {e2408583121}, pmid = {39401366}, issn = {1091-6490}, support = {IOS-2140427//NSF (NSF)/ ; IOS-2140428//NSF (NSF)/ ; IOS-2140429//NSF (NSF)/ ; IOS-2003205//NSF (NSF)/ ; IOS-2216855//NSF (NSF)/ ; DEB-1340852//NSF (NSF)/ ; DEB-1340856//NSF (NSF)/ ; DEB-2017895//NSF (NSF)/ ; }, mesh = {*Plant Leaves/physiology ; *Populus/physiology/genetics ; *Trees/physiology/genetics ; *Water ; Soil ; Genotype ; Extreme Heat ; Hot Temperature ; Ecosystem ; }, abstract = {Increasing heatwaves are threatening forest ecosystems globally. Leaf thermal regulation and tolerance are important for plant survival during heatwaves, though the interaction between these processes and water availability is unclear. Genotypes of the widely distributed foundation tree species Populus fremontii were studied in a controlled common garden during a record summer heatwave-where air temperature exceeded 48 °C. When water was not limiting, all genotypes cooled leaves 2 to 5 °C below air temperatures. Homeothermic cooling was disrupted for weeks following a 72-h reduction in soil water, resulting in leaf temperatures rising 3 °C above air temperature and 1.3 °C above leaf thresholds for physiological damage, despite the water stress having little effect on leaf water potentials. Tradeoffs between leaf thermal safety and hydraulic safety emerged but, regardless of water use strategy, all genotypes experienced significant leaf mortality following water stress. Genotypes from warmer climates showed greater leaf cooling and less leaf mortality after water stress in comparison with genotypes from cooler climates. These results illustrate how brief soil water limitation disrupts leaf thermal regulation and potentially compromises plant survival during extreme heatwaves, thus providing insight into future scenarios in which ecosystems will be challenged with extreme heat and unreliable soil water access.}, }
@article {pmid39399683, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39399683}, issn = {2693-5015}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, }
@article {pmid39399250, year = {2024}, author = {Arliyani, I and Noori, MT and Ammarullah, MI and Tangahu, BV and Mangkoedihardjo, S and Min, B}, title = {Constructed wetlands combined with microbial fuel cells (CW-MFCs) as a sustainable technology for leachate treatment and power generation.}, journal = {RSC advances}, volume = {14}, number = {44}, pages = {32073-32100}, pmid = {39399250}, issn = {2046-2069}, abstract = {The physical and chemical treatment processes of leachate are not only costly but can also possibly produce harmful by products. Constructed wetlands (CW) has been considered a promising alternative technology for leachate treatment due to less demand for energy, economic, ecological benefits, and simplicity of operations. Various trends and approaches for the application of CW for leachate treatment have been discussed in this review along with offering an informatics peek of the recent innovative developments in CW technology and its perspectives. In addition, coupling CW with microbial fuel cells (MFCs) has proven to produce renewable energy (electricity) while treating contaminants in leachate wastewaters (CW-MFC). The combination of CW-MFC is a promising bio electrochemical that plays symbiotic among plant microorganisms in the rhizosphere of an aquatic plant that convert sun electricity is transformed into bioelectricity with the aid of using the formation of radical secretions, as endogenous substrates, and microbial activity. Several researchers study and try to find out the application of CW-MFC for leachate treatment, along with this system and performance. Several key elements for the advancement of CW-MFC technology such as bioelectricity, reactor configurations, plant species, and electrode materials, has been comprehensively discussed and future research directions were suggested for further improving the performance. Overall, CW-MFC may offer an eco-friendly approach to protecting the aquatic environment and come with built-in advantages for visual appeal and animal habitats using natural materials such as gravel, soil, electroactive bacteria, and plants under controlled condition.}, }
@article {pmid39398940, year = {2024}, author = {Boyes, D and Hutchinson, F and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Common Flat-body moth, Agonopterix heracliana Linnaeus, 1758.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {329}, pmid = {39398940}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Agonopterix heracliana (the Common Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 539.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.36 kilobases in length.}, }
@article {pmid39398938, year = {2024}, author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Sinclair, E and Clayton-Lucey, IA and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , }, title = {The genome sequence of the heart cockle, Fragum sueziense (Issel, 1869).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {366}, pmid = {39398938}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual Fragum sueziense (the heart cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The genome sequence is 1,206.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 92.77 kilobases in length. Gene annotation of this assembly on Ensembl identified 70,309 protein-coding genes.}, }
@article {pmid39398937, year = {2024}, author = {Boyes, D and Crowley, LM and Morley, LM and , and , and , and , and , and , and , }, title = {The genome sequence of the Green Oak Leaf Roller, Tortrix viridana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {260}, pmid = {39398937}, issn = {2398-502X}, abstract = {We present a genome assembly from a female Tortrix viridana (the Green Oak Leaf Roller; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 456.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length.}, }
@article {pmid39396151, year = {2025}, author = {Burger, J and Gochfeld, M and Brown, KG and Cortes, M and Ng, K and Kosson, D}, title = {Using the National Land Cover Database as an indicator of shrub-steppe habitat: comparing two large United States federal lands with surrounding regions.}, journal = {Journal of toxicology and environmental health. Part A}, volume = {88}, number = {1}, pages = {1-19}, doi = {10.1080/15287394.2024.2412659}, pmid = {39396151}, issn = {1528-7394}, mesh = {*Ecosystem ; *Conservation of Natural Resources ; Idaho ; Washington ; Databases, Factual ; United States ; Grassland ; Environmental Monitoring/methods ; }, abstract = {There is a need to assess whether ecological resources are being protected on large, federal lands. The aim of this study was to present a methodology which consistently and transparently determines whether two large Department of Energy (U.S. DOE) facilities have protected valuable ecological lands on their sites compared to the surrounding region. The National Land Cover Database (2019) was used to examine the % shrub-scrub (shrub-steppe) and other habitats on the DOE's Hanford Site (HS, Washington) and on the Idaho National Laboratory (INL), compared to a 10-km and 30-km diameter band of land surrounding each site. On both sites, over 95% is in shrub-scrub or grassland, compared to the surrounding region. Approximately 70% of 10 km and 30-km bands around INL, and less than 50% of land surrounding HS is located in these two habitat types. INL has preserved a significantly higher % shrub/scrub habitat than HS, but INL allows grazing on 60% of its land. HS has preserved a significantly higher % grassland than INL but no grazing on site is present. The methodology presented may be used to compare key ecological habitat types such as grasslands, forest, and desert among sites in different parts of the country. This methodology enables managers, resource trustees, and the public to (1) make remediation decisions that protect resources, (2) assess whether landowners and managers have adequately characterized and protected environmental resources on their sites, and (3) whether landowners and managers have protected the integrity of that land as well as its climax vegetation.}, }
@article {pmid39395210, year = {2025}, author = {Pachade, S and Porwal, P and Kokare, M and Deshmukh, G and Sahasrabuddhe, V and Luo, Z and Han, F and Sun, Z and Qihan, L and Kamata, SI and Ho, E and Wang, E and Sivajohan, A and Youn, S and Lane, K and Chun, J and Wang, X and Gu, Y and Lu, S and Oh, YT and Park, H and Lee, CY and Yeh, H and Cheng, KW and Wang, H and Ye, J and He, J and Gu, L and Müller, D and Soto-Rey, I and Kramer, F and Arai, H and Ochi, Y and Okada, T and Giancardo, L and Quellec, G and Mériaudeau, F}, title = {RFMiD: Retinal Image Analysis for multi-Disease Detection challenge.}, journal = {Medical image analysis}, volume = {99}, number = {}, pages = {103365}, doi = {10.1016/j.media.2024.103365}, pmid = {39395210}, issn = {1361-8423}, mesh = {Humans ; *Retinal Diseases/diagnostic imaging ; Image Interpretation, Computer-Assisted/methods ; Deep Learning ; Fundus Oculi ; Datasets as Topic ; Diabetic Retinopathy/diagnostic imaging ; Databases, Factual ; }, abstract = {In the last decades, many publicly available large fundus image datasets have been collected for diabetic retinopathy, glaucoma, and age-related macular degeneration, and a few other frequent pathologies. These publicly available datasets were used to develop a computer-aided disease diagnosis system by training deep learning models to detect these frequent pathologies. One challenge limiting the adoption of a such system by the ophthalmologist is, computer-aided disease diagnosis system ignores sight-threatening rare pathologies such as central retinal artery occlusion or anterior ischemic optic neuropathy and others that ophthalmologists currently detect. Aiming to advance the state-of-the-art in automatic ocular disease classification of frequent diseases along with the rare pathologies, a grand challenge on "Retinal Image Analysis for multi-Disease Detection" was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI - 2021). This paper, reports the challenge organization, dataset, top-performing participants solutions, evaluation measures, and results based on a new "Retinal Fundus Multi-disease Image Dataset" (RFMiD). There were two principal sub-challenges: disease screening (i.e. presence versus absence of pathology - a binary classification problem) and disease/pathology classification (a 28-class multi-label classification problem). It received a positive response from the scientific community with 74 submissions by individuals/teams that effectively entered in this challenge. The top-performing methodologies utilized a blend of data-preprocessing, data augmentation, pre-trained model, and model ensembling. This multi-disease (frequent and rare pathologies) detection will enable the development of generalizable models for screening the retina, unlike the previous efforts that focused on the detection of specific diseases.}, }
@article {pmid39395131, year = {2024}, author = {Atesoglu, A and Ayyildiz, E and Karakaya, I and Bulut, FS and Serengil, Y}, title = {Land cover and drought risk assessment in Türkiye's mountain regions using neutrosophic decision support system.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {11}, pages = {1046}, pmid = {39395131}, issn = {1573-2959}, mesh = {*Droughts ; *Environmental Monitoring/methods ; *Climate Change ; Risk Assessment ; Ecosystem ; Turkey ; Decision Support Techniques ; Remote Sensing Technology ; Conservation of Natural Resources/methods ; }, abstract = {Earth observation (EO) provides dynamic scientific methods for tracking and defining ecological parameters in mountainous regions. Open-source platforms are frequently utilized in this context to efficiently collect and evaluate spatial data. In this study, we used Collect Earth (CE), an open-source land monitoring platform, to reveal and assess land cover, land cover change, and relevant ecological parameters such as drought risk. Mountain ecosystems were subject to an evaluation for the first time by combining remote sensing with a hybridization of Decision-Making Trial and Evaluation Laboratory (DEMATEL), analytic hierarchy process (AHP), and Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for neutrosophic sets in risk assessment problems of several connected criteria. The high and dispersed high alpine environment of Türkiye accommodates land with relatively less human influence, making it suitable to observe climate change impacts. In the framework of the study, we evaluated more than two decades (2000-2022) of land use and land cover (LULC) changes in the mountain regions of the country. Using nine identified ecological parameters, we also evaluated drought risk. The parameters included were the LULC classes and their change, elevation, slope, aspect, precipitation, temperature, normalized difference vegetation index (NDVI), water deficit, and evapotranspiration (ET). The risk map we produced revealed a high to very high drought risk for almost throughout the Türkiye's mountainous areas. We concluded that integrating geospatial techniques with hybridization is promising for mapping drought risk, helping policymakers prepare effective drought mitigation measures to reasonably adapt to climate change impacts.}, }
@article {pmid39392918, year = {2024}, author = {Kopania, EEK and Thomas, GWC and Hutter, CR and Mortimer, SME and Callahan, CM and Roycroft, E and Achmadi, AS and Breed, WG and Clark, NL and Esselstyn, JA and Rowe, KC and Good, JM}, title = {Sperm competition intensity shapes divergence in both sperm morphology and reproductive genes across murine rodents.}, journal = {Evolution; international journal of organic evolution}, volume = {79}, number = {1}, pages = {11-27}, pmid = {39392918}, issn = {1558-5646}, support = {DEB-1754096//National Science Foundation/ ; R01-HG009299/HG/NHGRI NIH HHS/United States ; R01-HD073439//National Institute of Child Health and Human Development/ ; }, mesh = {Animals ; Male ; *Spermatozoa/physiology ; Mice/genetics ; *Evolution, Molecular ; *Testis/anatomy & histology ; Phylogeny ; Selection, Genetic ; Sexual Selection ; Spermatogenesis/genetics ; Murinae/genetics/physiology ; Rats ; Reproduction/genetics ; }, abstract = {It remains unclear how variation in the intensity of sperm competition shapes phenotypic and molecular evolution across clades. Mice and rats in the subfamily Murinae are a rapid radiation exhibiting incredible diversity in sperm morphology and production. We combined phenotypic and genomic data to perform phylogenetic comparisons of male reproductive traits and genes across 78 murine species. We identified several shifts towards smaller relative testes mass (RTM), presumably reflecting reduced sperm competition. Several sperm traits were associated with RTM, suggesting that mating system evolution selects for convergent suites of traits related to sperm competitive ability. We predicted that sperm competition would also drive more rapid molecular divergence in species with large testes. Contrary to this, we found that many spermatogenesis genes evolved more rapidly in species with smaller RTM due to relaxed purifying selection. While some reproductive genes evolved rapidly under recurrent positive selection, relaxed selection played a greater role in underlying rapid evolution in small testes species. Our work demonstrates that postcopulatory sexual selection can impose strong purifying selection shaping the evolution of male reproduction and that broad patterns of molecular evolution may help identify genes that contribute to male fertility.}, }
@article {pmid39390673, year = {2024}, author = {Udaondo, Z and Ramos, JL and Abram, K}, title = {Unraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.}, journal = {FEMS microbiology reviews}, volume = {48}, number = {6}, pages = {}, pmid = {39390673}, issn = {1574-6976}, support = {PID2021-123469OB-I00//Plan Nacional sobre Drogas/ ; }, mesh = {*Pseudomonas putida/genetics/classification/drug effects ; *Genome, Bacterial/genetics ; *Genetic Variation ; Drug Resistance, Bacterial/genetics ; Genomics ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.}, }
@article {pmid39390511, year = {2024}, author = {Li, Y and Thomas, GWC and Richards, S and Waterhouse, RM and Zhou, X and Pfrender, ME}, title = {Rapid evolution of mitochondrion-related genes in haplodiploid arthropods.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {229}, pmid = {39390511}, issn = {1741-7007}, mesh = {Animals ; *Evolution, Molecular ; *Arthropods/genetics ; *Genes, Mitochondrial/genetics ; Phylogeny ; Haploidy ; Diploidy ; Oxidative Phosphorylation ; Cell Nucleus/genetics ; }, abstract = {BACKGROUND: Mitochondrial genes and nuclear genes cooperate closely to maintain the functions of mitochondria, especially in the oxidative phosphorylation (OXPHOS) pathway. However, mitochondrial genes among arthropod lineages have dramatic evolutionary rate differences. Haplodiploid arthropods often show fast-evolving mitochondrial genes. One hypothesis predicts that the small effective population size of haplodiploid species could enhance the effect of genetic drift leading to higher substitution rates in mitochondrial and nuclear genes. Alternatively, positive selection or compensatory changes in nuclear OXPHOS genes could lead to the fast-evolving mitochondrial genes. However, due to the limited number of arthropod genomes, the rates of evolution for nuclear genes in haplodiploid species, besides hymenopterans, are largely unknown. To test these hypotheses, we used data from 76 arthropod genomes, including 5 independently evolved haplodiploid lineages, to estimate the evolutionary rates and patterns of gene family turnover of mitochondrial and nuclear genes.
RESULTS: We show that five haplodiploid lineages tested here have fast-evolving mitochondrial genes and fast-evolving nuclear genes related to mitochondrial functions, while nuclear genes not related to mitochondrion showed no significant evolutionary rate differences. Among hymenopterans, bees and ants show faster rates of molecular evolution in mitochondrial genes and mitochondrion-related nuclear genes than sawflies and wasps. With genome data, we also find gene family expansions and contractions in mitochondrion-related genes of bees and ants.
CONCLUSIONS: Our results reject the small population size hypothesis in haplodiploid species. A combination of positive selection and compensatory changes could lead to the observed patterns in haplodiploid species. The elevated evolutionary rates in OXPHOS complex 2 genes of bees and ants suggest a unique evolutionary history of social hymenopterans.}, }
@article {pmid39387871, year = {2024}, author = {Smith, SJ and Cummins, SF and Motti, CA and Wang, T}, title = {A mass spectrometry database for the identification of marine animal saponin-related metabolites.}, journal = {Analytical and bioanalytical chemistry}, volume = {416}, number = {29}, pages = {6893-6907}, pmid = {39387871}, issn = {1618-2650}, mesh = {*Saponins/analysis/metabolism ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Mass Spectrometry/methods ; Databases, Factual ; }, abstract = {Saponins encompass a diverse group of naturally occurring glycoside molecules exhibiting amphiphilic properties and a broad range of biological activities. There is a resurgence of interest in those saponins produced by marine organisms based on their potential therapeutic benefits, application in food products and most recently their potential involvement in intra- and inter-species chemical communication. The continual advancements in liquid chromatography techniques and mass spectrometry technologies have allowed for greater detection rates, as well as improved isolation and elucidation of saponins. These factors have significantly contributed to the expansion in the catalogue of known saponin structures isolated from marine invertebrates; however, there currently exists no specific chemical library resource to accelerate the discovery process. In this study, a Marine Animal Saponin Database (MASD v1.0) has been developed to serve as a valuable chemical repository for known marine saponin-related data, including chemical formula, molecular mass and biological origin of nearly 1000 secondary metabolites associated with saponins produced by marine invertebrates. We demonstrate its application with an exemplar asteroid extract (Acanthaster cf. solaris, also known as crown-of-thorns starfish; COTS), identifying saponins from the MASD v1.0 that have been previously reported from COTS, as well as 21 saponins isolated from multiple other related asteroid species. This database will help facilitate future research endeavours, aiding researchers in exploring the vast chemical diversity of saponins produced by marine organisms and providing ecological insights, and the realisation of their potential for various applications, including as pharmaceuticals.}, }
@article {pmid39386964, year = {2024}, author = {Martin, SH and Lohse, K and Ebdon, S and Mackintosh, A and , and , and , and , and , }, title = {The genome sequence of the Pearl-bordered Fritillary, Boloria euphrosyne (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {267}, pmid = {39386964}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Boloria euphrosyne (the Pearl-bordered Fritillary; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 400.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.17 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,138 protein coding genes.}, }
@article {pmid39385455, year = {2024}, author = {Wu, H and Li, Q and Wu, JC}, title = {Bioinformatics-aided function exploration of GH29 fucosidases from human gut Parabacteroides.}, journal = {Glycobiology}, volume = {34}, number = {12}, pages = {}, doi = {10.1093/glycob/cwae086}, pmid = {39385455}, issn = {1460-2423}, support = {2023GDASZH-2023010102//GDAS' Project of Science and Technology Development/ ; SL2023A04J01435//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022A1515110917//Guangdong Basic and Applied Basic Research Foundation/ ; 32302033//National Natural Science Foundation of China/ ; 2023A04J1494//Guangzhou Basic and Applied Basic Research Foundation/ ; 2022GDASZH-2022010110//GDAS' Project of Science and Technology Development/ ; }, mesh = {Humans ; *alpha-L-Fucosidase/metabolism/genetics/chemistry ; *Computational Biology ; Gastrointestinal Microbiome ; Bacteroidetes/enzymology/genetics ; Polysaccharides/metabolism/chemistry ; Substrate Specificity ; Mucins/metabolism/chemistry ; }, abstract = {Gut microbes produce α-l-fucosidases critical for utilizing human milk oligosaccharides, mucosal and dietary glycans. Although gut Parabacteroides have garnered attention for their impact on host health and disease, their CAZymes remain poorly studied. CAZome analysis of eleven gut Parabacteroides type strains revealed their capacity to degrade mucin O-glycans. Their abundance of GH29 fucosidases caught our attention, and we predicted the functional profiles of 46 GH29 fucosidases using in silico approaches. Our findings showed diverse linkages specificities and species-specific distributions, with over half of GH29 enzymes functioning as α1,3/4 fucosidases, essential for acting on Lewis antigen epitopes of mucin O-glycans. We further enzymatically validated 4 novel GH29 sequences from poorly characterized groups. PgoldGH29A (cluster37GH29BERT, GH29:75.1CUPP) does not act on tested natural substrates. PgoldGH29B (cluster1GH29BERT, GH29:84.1CUPP) functions as a strict α1,3/4 fucosidase. PgoldGH29C (cluster14GH29BERT, GH29:29.1CUPP) displays unprecedented substrate specificity for α1,2/3/4 disaccharides. PgoldGH29D (cluster4GH29BERT, GH29:6.2CUPP) acts on α1,2/3/4/6 linkages similar to enzymes from GH29:6.1CUPP but prefers disaccharides over trisaccharides. These results suggest that PgoldGH29B and PgoldGH29D can contribute to mucin O-glycan degradation via their α1,3/4 and α1,2 fucosidase activity, respectively, while the natural substrates of PgoldGH29A and PgoldGH29C may be irrelevant to host-glycans. These insights enhance our understanding of the ecological niches inhabited by gut Parabacteroides and may guide similar exploration in other intriguing gut microbial species.}, }
@article {pmid39381069, year = {2024}, author = {Boyes, D and Lees, DC and Sims, I and Phillips, D and Boyes, C and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Yellow-dotted Stilt, Euspilapteryx auroguttella Stephens, 1835.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {226}, pmid = {39381069}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Euspilapteryx auroguttella (the Yellow-dotted Stilt; Arthropoda; Insecta; Lepidoptera; Gracillariidae). The genome sequence is 331.9 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.94 kilobases in length.}, }
@article {pmid39379720, year = {2024}, author = {Klopper, A}, title = {GPS tracking reveals how hares shape lynx populations.}, journal = {Nature}, volume = {634}, number = {8033}, pages = {301}, doi = {10.1038/d41586-024-03272-x}, pmid = {39379720}, issn = {1476-4687}, mesh = {Animals ; *Geographic Information Systems ; *Lynx/physiology ; Population Density ; Population Dynamics ; Alaska ; *Predatory Behavior ; *Hares/physiology ; }, }
@article {pmid39376700, year = {2024}, author = {Chelliah, DS and Ray, AE and Zhang, E and Terauds, A and Ferrari, BC}, title = {The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1443491}, pmid = {39376700}, issn = {1664-302X}, abstract = {Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 [-], SO4 [2-], SO3) were found at Old Wallow, with conductivity and Cl[-] levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 [2-], pH, and SO3, and for bacteria with moisture, Na2O, and Cl[-]. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.}, }
@article {pmid39374677, year = {2024}, author = {Ikeda, T and Cooray, U and Matsugaki, R and Suzuki, Y and Takagi, M and Muramatsu, K and Fushimi, K and Murakami, M and Osaka, K and Matsuda, S}, title = {Associations of hypothetical early intensive in-hospital rehabilitation with activities of daily living after hip fracture surgery in patients with and without dementia: emulating a randomized controlled trial using medical claims data.}, journal = {Journal of clinical epidemiology}, volume = {176}, number = {}, pages = {111550}, doi = {10.1016/j.jclinepi.2024.111550}, pmid = {39374677}, issn = {1878-5921}, mesh = {Humans ; *Hip Fractures/surgery/rehabilitation ; Female ; Male ; *Dementia/rehabilitation ; Aged ; *Activities of Daily Living ; Japan ; Aged, 80 and over ; Middle Aged ; Hospitalization/statistics & numerical data ; Recovery of Function ; }, abstract = {OBJECTIVES: To investigate the impact of early intensive in-hospital rehabilitation, initiated within 2 days of surgery and lasting up to 7 days, on the recovery of activities of daily living in patients with and without dementia.
STUDY DESIGN AND SETTING: Medical claims data from 925 hospitals in Japan were analyzed. We enrolled patients aged ≥50 years who underwent hip fracture surgery within 2 days of admission between April 1, 2018, and December 31, 2019. Low- (20 minutes per day starting on day 2), highest- (60 minutes per day starting on day 1), and gradually increasing (20 minutes on day 1, 40 minutes on days 2-4, and 60 minutes per day thereafter) intensity regimens were used as exposures. The outcomes were Barthel Index (BI) scores at 14 and 30 days postoperatively. For per-protocol analysis, a target trial emulation framework with the sequential doubly robust estimator was used.
RESULTS: Among patients without dementia (N = 11,461), no significant differences in BI scores were observed at 14 days postoperatively across regimens. At 30 days postoperatively, significant differences in BI scores were noted between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 15.2 (95% CI, 10.7-19.7) and 14.7 (95% CI, 9.2-20.2), respectively. In patients with dementia (N = 14,302), significant differences in BI scores were noted at 14 days postoperatively between highest- and low-intensity regimens and between gradually increasing intensity and low-intensity regimens, with additive BI scores of 8.7 (95% CI, 5.2-12.2) and 10.7 (95% CI, 5.8-15.6), respectively. At 30 days postoperatively, a significant difference in BI scores was observed between gradually increasing intensity and low-intensity regimens, with an additive BI score of 17.9 (95% CI, 11.3-24.5).
CONCLUSION: Early intensive in-hospital rehabilitation is highly relevant and beneficial for dementia patients.}, }
@article {pmid39373887, year = {2024}, author = {Dittrich, SP and Adithya, S and Ajith, Y and Athira, N and Athira, KS and Safeer, MS and Preena, P and Aishwarya, A and Athira, K and Nisha, AR and Devi, G and Mäder, M and Beena, V and Jacob, SS}, title = {Parasite diversity among domestic goats of tropical monsoon climatic zone in India.}, journal = {Parasitology research}, volume = {123}, number = {10}, pages = {342}, pmid = {39373887}, issn = {1432-1955}, support = {IN-ME_BI-5550//Deutscher Akademischer Austauschdienst/ ; SRG/2022/000837//Science and Engineering Research Board/ ; SRG/2022/000837//Science and Engineering Research Board/ ; }, mesh = {Animals ; *Goats/parasitology ; India/epidemiology ; *Goat Diseases/parasitology/epidemiology ; *Tropical Climate ; Phylogeny ; Parasitic Diseases, Animal/parasitology/epidemiology ; Parasites/classification/isolation & purification/genetics ; Biodiversity ; }, abstract = {Among different climatic zones in India, the tropical monsoon region comprises a diverse ecosystem characterized by the endemic nature of several parasites including certain emerging and re-emerging vector-borne pathogens of humans, whereas a systematic investigation of the occurrence of different parasites among domestic goats in this area is not yet explored. The goal of the present study is to explore the parasite diversity focusing on molecular identification of vector-borne hemoparasites and its health impacts on domestic goats reared in the tropical monsoon climate zone of Kerala, India. Among 227 goats presented to the Teaching Veterinary Clinical Complex (TVCC) in the monsoon months of 2023, thirty animals were recruited for the study. The animals were screened for the presence of different hemoparasites (Anaplasma spp., Theileria spp., and Babesia spp.), ectoparasites (ticks, lice, and fleas), and gastrointestinal (GI) parasites (hookworms, threadworms, tapeworms, whipworms, and coccidia). The isolated hemoparasites were further characterized by sequencing and phylogenetic analysis. The correlation studies to elucidate the association between the occurrence of different parasites and clinical manifestations (hyperthermia, pallor of mucous membrane, circulatory failure, respiratory signs, neurological instability, and GI signs), blood picture (anemia, leukopenia, thrombocytopenia), demographics (sex and age), and treatment history (hemoparasitic therapy, ectoparasiticidal application, and prophylactic deworming) were conducted. The co-infection status of these parasites was also evaluated. A substantial portion of the goats in the study group was found to be affected by vector-borne hemoparasitic diseases and their arthropod vectors or GI parasites or both. This can be attributed to the constantly warm and humid climate of the region, which is favorable for the survival and growth of different life cycle stages of these parasites and vectors. A strategic parasitic disease surveillance-cum-control program is the need of the hour for ensuring climate resilience and profitable goat farming in the region.}, }
@article {pmid39373528, year = {2024}, author = {Ros-Rocher, N}, title = {The evolution of multicellularity and cell differentiation symposium: bridging evolutionary cell biology and computational modelling using emerging model systems.}, journal = {Biology open}, volume = {13}, number = {10}, pages = {}, pmid = {39373528}, issn = {2046-6390}, support = {101106415//European Union's Horizon Europe research and innovation funding program/ ; //Institute Pasteur: Institut Pasteur; Baylor College of Medicine/ ; }, mesh = {*Cell Differentiation/genetics ; *Biological Evolution ; Animals ; Computational Biology/methods ; Humans ; Cell Biology ; Models, Biological ; Computer Simulation ; Genomics/methods ; }, abstract = {'The evolution of multicellularity and cell differentiation' symposium, organized as part of the EuroEvoDevo 2024 meeting on June 25-28th in Helsinki (Finland), addressed recent advances on the molecular and mechanistic basis for the evolution of multicellularity and cell differentiation in eukaryotes. The symposium involved over 100 participants and brought together 10 speakers at diverse career stages. Talks covered various topics at the interface of developmental biology, evolutionary cell biology, comparative genomics, computational biology, and ecology using animal, protist, algal and mathematical models. This symposium offered a unique opportunity for interdisciplinary dialog among researchers working on different systems, especially in promoting collaborations and aligning strategies for studying emerging model species. Moreover, it fostered opportunities to promote early career researchers in the field and opened discussions of ongoing work and unpublished results. In this Meeting Review, we aim to promote the research, capture the spirit of the meeting, and present key topics discussed within this dynamic, growing and open community.}, }
@article {pmid39373052, year = {2024}, author = {Xie, X and Gui, L and Qiao, B and Wang, G and Huang, S and Zhao, Y and Sun, S}, title = {Deep learning in template-free de novo biosynthetic pathway design of natural products.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {6}, pages = {}, pmid = {39373052}, issn = {1477-4054}, support = {2572022BD04//Fundamental Research Funds for the Central Universities/ ; 62001088//National Natural Science Foundation of China/ ; }, mesh = {*Biological Products/metabolism ; *Deep Learning ; *Biosynthetic Pathways ; Algorithms ; Computational Biology/methods ; Humans ; }, abstract = {Natural products (NPs) are indispensable in drug development, particularly in combating infections, cancer, and neurodegenerative diseases. However, their limited availability poses significant challenges. Template-free de novo biosynthetic pathway design provides a strategic solution for NP production, with deep learning standing out as a powerful tool in this domain. This review delves into state-of-the-art deep learning algorithms in NP biosynthesis pathway design. It provides an in-depth discussion of databases like Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and UniProt, which are essential for model training, along with chemical databases such as Reaxys, SciFinder, and PubChem for transfer learning to expand models' understanding of the broader chemical space. It evaluates the potential and challenges of sequence-to-sequence and graph-to-graph translation models for accurate single-step prediction. Additionally, it discusses search algorithms for multistep prediction and deep learning algorithms for predicting enzyme function. The review also highlights the pivotal role of deep learning in improving catalytic efficiency through enzyme engineering, which is essential for enhancing NP production. Moreover, it examines the application of large language models in pathway design, enzyme discovery, and enzyme engineering. Finally, it addresses the challenges and prospects associated with template-free approaches, offering insights into potential advancements in NP biosynthesis pathway design.}, }
@article {pmid39367377, year = {2024}, author = {Qiao, L and Zhang, C and Zhang, M and Jiang, H and Shi, Y and Zhang, W and Mei, Y and Li, Y and Wang, H}, title = {High-risk spatiotemporal patterns of leprosy in the southeastern region of Yunnan province from 2010 to 2022: an analysis at the township level.}, journal = {BMC public health}, volume = {24}, number = {1}, pages = {2707}, pmid = {39367377}, issn = {1471-2458}, support = {82103748//National Natural Science Foundation of China/ ; 81972950//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Leprosy/epidemiology ; China/epidemiology ; Female ; Male ; *Spatio-Temporal Analysis ; Adult ; Middle Aged ; *Geographic Information Systems ; Adolescent ; Young Adult ; Aged ; Child ; Risk Factors ; }, abstract = {BACKGROUND: Despite being preventable and curable, leprosy remains endemic in some undeveloped regions, including China. Wenshan Zhuang and Miao Autonomous Prefecture (Wenshan prefecture) currently bears the highest leprosy burden in China. In this ecological study, we aimed to analyze the epidemiological characteristics as well as identify and visualize the high-risk townships of Wenshan prefecture using the most updated leprosy data from 2010 to 2022.
METHODS: Geographical information system combined with spatial scan statistics was used for newly detected leprosy cases abstracted from the Leprosy Management Information System in China. Global Moran's I index was used to uncover the spatial pattern of leprosy at the township level. Spatial scan statistics, encompassing purely temporal, purely spatial, spatial variation in temporal trends, and space-time analysis, were implemented for detecting the risk clusters.
RESULTS: Between 2010 and 2022, Wenshan prefecture detected 532 new leprosy cases, comprising 352 (66.17%) males and 180 (33.83%) females. The aggregated time primarily occurred between October 2010 and March 2014. The distribution pattern of newly detected leprosy cases was spatially clustered. We identified four high-risk spatial clusters encompassing 54.51% of the new cases. Furthermore, spatial variation in temporal trends highlighted one cluster as a potential high-risk area. Finally, two space-time clusters were detected, and the most likely cluster was predominantly located in the central and northwest regions of Wenshan prefecture, spanning from January 2010 to September 2013.
CONCLUSIONS: In this ecology study, we characterized the epidemiological features and temporal and spatial patterns of leprosy in Wenshan prefecture using the most recent leprosy data between 2010 and 2022. Our findings offer scientific insights into the epidemiological profiles and spatiotemporal dynamics of leprosy in Wenshan prefecture. Clinicians and policymakers should pay particular attention to the identified clusters for the prevention and control of leprosy.}, }
@article {pmid39367017, year = {2024}, author = {Zhou, M and Guo, F}, title = {Mechanism and spatial spillover effect of digital economy on common prosperity in the Yellow River Basin of China.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {23086}, pmid = {39367017}, issn = {2045-2322}, support = {41801105//National Natural Science Foundation of China/ ; 2022RW040//Shandong Province Higher Education Youth Innovation Technology Support Program/ ; 23CGLJ15//Shandong Province Social Science Planning and Research Project/ ; }, abstract = {The digital economy has emerged as a new trend in economic development and has profoundly influenced the process of achieving common prosperity. However, current research on the correlation between the digital economy and common prosperity from the perspective of a river basin still needs to be strengthened. Based on this, the present study first theoretically elaborates the conceptual meanings of "digital economy" and "common prosperity", as well as the mechanism by which the digital economy empowers common prosperity. Subsequently, a scientifically-constructed performance evaluation index system for the digital economy and common prosperity is established. Considering the Yellow River Basin as an empirical case study area, this study investigates the mechanism and spatial spillover effects of the digital economy in empowering common prosperity from 2005 to 2020. The research findings reveal that: (1) The Yellow River Basin exhibits a basin characteristic with downstream > midstream > upstream areas regarding the level of common prosperity and digital economy. It indicates that a distinct spatial correlation exists between the two factors. However, the ongoing decrease in both high-level and very high-level areas reflects the lengthy and challenging journey of enhancing the quality and efficiency of the digital economy in empowering common prosperity. (2) The digital economy not only directly impacts common prosperity, but also fosters its development through spatial spillover effects. Among the control factors, informatization and housing levels have a major stimulating effect. (3) There exists a clear regional heterogeneity in how the digital economy affects common prosperity in the Yellow River Basin. Specifically, common prosperity of downstream cities is significantly impacted by the digital economy. The spatial spillover effects of the digital economy on common prosperity exhibit a pronounced "neighborhood as a moat" characteristic. (4) The digital economy facilitates the achievement of shared prosperity through the implementation of mechanisms centered on sharing, affluence, and sustainability. These research findings illuminate the empowering mechanisms and spatial spillover pathways of the digital economy in promoting shared prosperity, aligning with national strategies for ecological conservation and high-quality development in the Yellow River Basin.}, }
@article {pmid39364368, year = {2024}, author = {Bullion, CM and Bahlai, CA}, title = {Data gap or biodiversity gap? Evaluating apparent spatial biases in community science observations of Odonata in the east-central United States.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18115}, pmid = {39364368}, issn = {2167-8359}, mesh = {Animals ; *Biodiversity ; *Odonata ; Humans ; Bias ; United States ; Databases, Factual ; }, abstract = {Odonates (dragonflies and damselflies) have become popular study organisms for insect-based climate studies, due to the taxon's strong sensitivity to environmental conditions, and an enthusiastic following by community scientists due to their charismatic appearance and size. Where formal records of this taxon can be limited, public efforts have provided nearly 1,500,000 open-sourced odonate records through online databases, making real-time spatio-temporal monitoring more feasible. While these databases can be extensive, concerns regarding these public endeavors have arisen from a variety of sources: records may be biased by human factors (ex: density, technological access) which may cause erroneous interpretations. Indeed, records of odonates in the east-central US documented in the popular database iNaturalist bear striking patterns corresponding to political boundaries and other human activities. We conducted a 'ground-truthing' study using a structured sampling method to examine these patterns in an area where community science reports indicated variable abundance, richness, and diversity which appeared to be linked to observation biases. Our observations were largely consistent with patterns recorded by community scientists, suggesting these databases were indeed capturing representative biological trends and raising further questions about environmental drivers in the observed data gaps.}, }
@article {pmid39363544, year = {2024}, author = {Panayi, P and Peters, E and Bentall, R and Hardy, A and Berry, K and Sellwood, W and Dudley, R and Longden, E and Underwood, R and Steel, C and Jafari, H and Emsley, R and Mason, L and Elliott, R and Varese, F}, title = {Complex PTSD symptoms predict positive symptoms of psychosis in the flow of daily life.}, journal = {Psychological medicine}, volume = {54}, number = {12}, pages = {1-12}, pmid = {39363544}, issn = {1469-8978}, support = {NIHR128623//Health Technology Assessment Programme/ ; NIHR130971//Efficacy and Mechanism Evaluation Programme/ ; N/A//NIHR Maudsley Biomedical Research Centre/ ; }, abstract = {BACKGROUND: Post-traumatic stress disorder (PTSD) has been shown to predict psychotic symptomology. However, few studies have examined the relative contribution of PTSD compared to broader post-traumatic sequelae in maintaining psychosis. Complex PTSD (cPTSD), operationalized using ICD-11 criteria, includes core PTSD (intrusions, avoidance, hyperarousal) as well as additional "disturbances of self-organisation" (DSO; emotional dysregulation, interpersonal difficulties, negative self-concept) symptoms, more likely to be associated with complex trauma histories. It was hypothesized that DSOs would be associated with positive psychotic symptoms (paranoia, voices, and visions) in daily life, over and above core PTSD symptoms.
METHODS: This study (N = 153) employed a baseline subsample of the Study of Trauma And Recovery (STAR), a clinical sample of participants with comorbid post-traumatic stress and psychosis symptoms. Core PTSD, DSO and psychosis symptoms were assessed up to 10 times per day at quasi-random intervals over six consecutive days using Experience Sampling Methodology.
RESULTS: DSOs within the preceding 90 min predicted paranoia, voices, and visions at subsequent moments. These relationships persisted when controlling for core PTSD symptoms within this timeframe, which were themselves significant. The associations between DSOs and paranoia but not voices or visions, were significantly stronger than those between psychosis and core PTSD symptoms.
CONCLUSIONS: Consistent with an affective pathway to psychosis, the findings suggest that DSOs may be more important than core PTSD symptoms in maintaining psychotic experiences in daily life among people with comorbid psychosis and cPTSD, and indicate the potential importance of addressing broad post-traumatic sequelae in trauma-focused psychosis interventions.}, }
@article {pmid39363203, year = {2024}, author = {Viana, PAB and Tschoeke, DA and de Moraes, L and Santos, LA and Barral-Netto, M and Khouri, R and Ramos, PIP and Meirelles, PM}, title = {Design and implementation of a metagenomic analytical pipeline for respiratory pathogen detection.}, journal = {BMC research notes}, volume = {17}, number = {1}, pages = {291}, pmid = {39363203}, issn = {1756-0500}, support = {2023-PPI-007//Rockefeller Foundation/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/microbiology/diagnosis ; Metagenome/genetics ; Computational Biology/methods ; Reproducibility of Results ; Nasopharynx/microbiology/virology ; }, abstract = {OBJECTIVE: We developed an in-house bioinformatics pipeline to improve the detection of respiratory pathogens in metagenomic sequencing data. This pipeline addresses the need for short-time analysis, high accuracy, scalability, and reproducibility in a high-performance computing environment.
RESULTS: We evaluated our pipeline using ninety synthetic metagenomes designed to simulate nasopharyngeal swab samples. The pipeline successfully identified 177 out of 204 respiratory pathogens present in the compositions, with an average processing time of approximately 4 min per sample (processing 1 million paired-end reads of 150 base pairs). For the estimation of all the 470 taxa included in the compositions, the pipeline demonstrated high accuracy, identifying 420 and achieving a correlation of 0.9 between their actual and predicted relative abundances. Among the identified taxa, 27 were significantly underestimated or overestimated, including only three clinically relevant pathogens. We also validated the pipeline by applying it to a clinical dataset from a study on metagenomic pathogen characterization in patients with acute respiratory infections and successfully identified all pathogens responsible for the diagnosed infections. These findings underscore the pipeline's effectiveness in pathogen detection and highlight its potential utility in respiratory pathogen surveillance.}, }
@article {pmid39362872, year = {2024}, author = {Fu, SW and Feng, MC and Chi, PW and Ding, TS}, title = {Combining citizen science data and literature to build a traits dataset of Taiwan's birds.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1076}, pmid = {39362872}, issn = {2052-4463}, mesh = {Animals ; Taiwan ; *Birds ; *Citizen Science ; *Ecosystem ; Databases, Factual ; }, abstract = {Trait-based methodologies are gaining traction in the field of ecology, providing deeper insights into ecosystem structure and functions. To this end, trait databases tailored to specific taxonomic groups have become foundational. In Taiwan, the collaborative efforts of avian researchers and dedicated citizen scientists have led to the compilation of a vast array of data. This includes web-sourced images from social media, spatial distribution records from eBird, and morphological metrics from banded birds and specimens. Enriched by peer-reviewed literature, we have meticulously assembled a comprehensive trait dataset encompassing 454 bird species across 73 families. This dataset covers a wide range of traits, including foraging ecology, morphological characteristics, territorial behaviors, breeding attributes, and the roles of bird species in ecosystem regulation. As an invaluable resource, this dataset lays the foundation for in-depth exploration of functional diversity, trait-based community ecology, ecosystem function, and critical insights needed to shape conservation strategies.}, }
@article {pmid39362167, year = {2024}, author = {Fardullah, M and Hossain, MT and Islam, MS and Islam, MR and Rahman, MR and Akther, K and Uddin, A and Morshed, S and Sultana, N and Alam, MA and Bahadur, NM and Robel, FN}, title = {Occurrence and spatial distribution of microplastics in water and sediments of Hatiya Island, Bangladesh and their risk assessment.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122697}, doi = {10.1016/j.jenvman.2024.122697}, pmid = {39362167}, issn = {1095-8630}, mesh = {*Microplastics/analysis ; Risk Assessment ; Bangladesh ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry/analysis ; Islands ; }, abstract = {This research has evaluated the MPs distribution, characteristics, and potential threats of MPs in surface water and sediments from Hatiya Island. The results showed that the abundance of MPs was 139 ± 44 items/m[3] in surface water and 493 ± 80 items/kg dw in sediments, indicating higher levels of MPs contamination in sediment samples. Fibers were the predominant kind of microplastics, and microscopic sizes (0.3-1.5 mm) MPs were generally more frequent and largely present in both the surface water and sediments. Fourier-transform infrared spectroscopy (FTIR) confirmed that polyethylene terephthalate was the major polymer component of microplastics in surface water, whereas polyethylene was the most abundant polymer in sediments. MPs contamination risk was examined based on multiple risk assessment models. Nemerow pollution index (NPI) and pollutant load index (PLI) show minimal pollution levels of MPs. But potential hazard index (PHI), potential ecological risk factor (Er), and potential ecological risk index (RI), indicate severe MPs contamination due to the presence of polyurethane, polycarbonate, polyvinyl chloride, epoxy that were hazardous MPs and exhibited a critical concern for MPs risk. These statistics will help to understand the environmental difficulties generated by MPs and which hazard is waiting for mankind in the future.}, }
@article {pmid39360250, year = {2024}, author = {Soni, N and Eyre, MT and Souza, FN and Diggle, PJ and Ko, AI and Begon, M and Pickup, R and Childs, JE and Khalil, H and Carvalho-Pereira, TSA and Pertile, AC and Carvalho, M and de Oliveira, D and Nery, N and Giorgi, E and Costa, F}, title = {Disentangling the influence of reservoir abundance and pathogen shedding on zoonotic spillover of the Leptospira agent in urban informal settlements.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1447592}, pmid = {39360250}, issn = {2296-2565}, mesh = {Animals ; Humans ; *Leptospirosis/epidemiology/microbiology/transmission ; *Leptospira/isolation & purification ; *Disease Reservoirs/microbiology ; Brazil/epidemiology ; Rats ; *Zoonoses/microbiology ; Male ; Female ; Adult ; Bacterial Shedding ; Longitudinal Studies ; Middle Aged ; Risk Factors ; Urban Population/statistics & numerical data ; Adolescent ; Young Adult ; }, abstract = {Rats are major reservoirs for pathogenic Leptospira, the bacteria causing leptospirosis, particularly in urban informal settlements. However, the impact of variation in rat abundance and pathogen shedding rates on spillover transmission to humans remains unclear. This study aimed to investigate how spatial variation in reservoir abundance and pathogen pressure affect Leptospira spillover transmission to humans in a Brazilian urban informal settlement. A longitudinal eco-epidemiological study was conducted from 2013 to 2014 to characterize the spatial distribution of rat abundance and Leptospira shedding rates in rats and determine the association with human infection risk in a cohort of 2,206 community residents. Tracking plates and live-trapping were used to measure rat abundance and quantify rat shedding status and load. In parallel, four sequential biannual serosurveys were used to identify human Leptospira infections. To evaluate the role of shedding on human risk, we built three statistical models for: (1) the relative abundance of rats, (2) the shedding rate by individual rats, and (3) human Leptospira infection, in which "total shedding", obtained by multiplying the predictions from those two models, was used as a risk factor. We found that Leptospira shedding was associated with older and sexually mature rats and varied spatially and temporally-higher at valley bottoms and with seasonal rainfall (December to March). The point estimate for "total shedding" by rat populations was positive, i.e., Leptospira infection risk increased with total shedding, but the association was not significant [odds ratio (OR) = 1.1; 95% confidence interval (CI): 0.9, 1.4]. This positive trend was mainly driven by rat abundance, rather than individual rat shedding (OR = 1.8; 95% CI: 0.6, 5.4 vs. OR = 1.0; 95% CI: 0.7, 1.4]. Infection risk was higher in areas with more vegetative land cover (OR = 2.4; 95% CI: 1.2, 4.8), and when floodwater entered the house (OR = 2.4; 95% CI: 1.6, 3.4). Our findings indicate that environmental and hydrological factors play a more significant role in Leptospira spillover than rat associated factors. Furthermore, we developed a novel approach combining several models to elucidate complex links between animal reservoir abundance, pathogen shedding and environmental factors on zoonotic spillover in humans that can be extended to other environmentally transmitted diseases.}, }
@article {pmid39359327, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Crescent Plume, Marasmarcha lunaedactyla (Haworth, 1811).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {431}, pmid = {39359327}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Marasmarcha lunaedactyla (the Crescent Plume; Arthropoda; Insecta; Lepidoptera; Pterophoridae). The genome sequence is 771.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 16.43 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,571 protein coding genes.}, }
@article {pmid39355992, year = {2024}, author = {Auffret, AG and Ladouceur, E and Haussmann, NS and Daouti, E and Elumeeva, TG and Kačergytė, I and Knape, J and Kotowska, D and Low, M and Onipchenko, VG and Paquet, M and Rubene, D and Plue, J}, title = {A global database of soil seed bank richness, density, and abundance.}, journal = {Ecology}, volume = {105}, number = {11}, pages = {e4438}, doi = {10.1002/ecy.4438}, pmid = {39355992}, issn = {1939-9170}, mesh = {*Seed Bank ; *Soil ; *Databases, Factual ; *Biodiversity ; *Seeds ; Ecosystem ; Plants/classification ; }, abstract = {A soil seed bank is the collective name for viable seeds that are stored naturally in the soil. At the species or population level, the ability to form a seed bank represents a strategy for (re)colonization following a disturbance or other change in the local environmental conditions. At the community level, seed banks are thought to buffer local diversity during periods of environmental change and are often studied in relation to the potential for passive habitat restoration. The role that seed banks play in plant population and community dynamics, as well as their importance in the agricultural sector, means that they have been widely studied in ecological research. This database is the result of a comprehensive literature search, including all seed bank studies from the Web of Science from which data could be extracted, as well as an additional search of the Russian language literature. The database contains information on the species richness, seed density, and/or seed abundance in 3096 records from at least 1929 locations across the world's seven continents, extracted from 1442 studies published between 1940 and 2020. Records are grouped into five broad habitat categories (aquatic, arable, forest, grassland-including shrubland-and wetland), including information relating to habitat degradation from, or restoration to other habitats (total 14 combinations). Sampling protocols were also extracted for each record, and the database was extensively checked for errors. The location of each record was then used to extract summary climate data and biome classification from external published databases. The database has several potential uses. The large geographical spread relative to many other global biodiversity datasets is relevant for investigating patterns of diversity in biogeographical or macroecological contexts. Habitat type and status (intact, degraded, and restored) can be used to provide insights for biodiversity conservation, while the potential effects of sampling method and effort can be used to inform optimized data collection for future seed bank studies. This database is released under the CC-BY license.}, }
@article {pmid39354608, year = {2024}, author = {Navratilova, HF and Whetton, AD and Geifman, N}, title = {Artificial intelligence driven definition of food preference endotypes in UK Biobank volunteers is associated with distinctive health outcomes and blood based metabolomic and proteomic profiles.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {881}, pmid = {39354608}, issn = {1479-5876}, support = {202205080261//Lembaga Pengelola Dana Pendidikan/ ; }, mesh = {Humans ; *Food Preferences ; United Kingdom ; Male ; Female ; *Biological Specimen Banks ; Middle Aged ; *Proteomics/methods ; *Metabolomics ; *Artificial Intelligence ; Metabolome ; Adult ; Aged ; Surveys and Questionnaires ; Health ; UK Biobank ; }, abstract = {BACKGROUND: Specific food preferences can determine an individual's dietary patterns and therefore, may be associated with certain health risks and benefits.
METHODS: Using food preference questionnaire (FPQ) data from a subset comprising over 180,000 UK Biobank participants, we employed Latent Profile Analysis (LPA) approach to identify the main patterns or profiles among participants. blood biochemistry across groups/profiles was compared using the non-parametric Kruskal-Wallis test. We applied the Limma algorithm for differential abundance analysis on 168 metabolites and 2923 proteins, and utilized the Database for Annotation, Visualization and Integrated Discovery (DAVID) to identify enriched biological processes and pathways. Relative risks (RR) were calculated for chronic diseases and mental conditions per group, adjusting for sociodemographic factors.
RESULTS: Based on their food preferences, three profiles were termed: the putative Health-conscious group (low preference for animal-based or sweet foods, and high preference for vegetables and fruits), the Omnivore group (high preference for all foods), and the putative Sweet-tooth group (high preference for sweet foods and sweetened beverages). The Health-conscious group exhibited lower risk of heart failure (RR = 0.86, 95%CI 0.79-0.93) and chronic kidney disease (RR = 0.69, 95%CI 0.65-0.74) compared to the two other groups. The Sweet-tooth group had greater risk of depression (RR = 1.27, 95%CI 1.21-1.34), diabetes (RR = 1.15, 95%CI 1.01-1.31), and stroke (RR = 1.22, 95%CI 1.15-1.31) compared to the other two groups. Cancer (overall) relative risk showed little difference across the Health-conscious, Omnivore, and Sweet-tooth groups with RR of 0.98 (95%CI 0.96-1.01), 1.00 (95%CI 0.98-1.03), and 1.01 (95%CI 0.98-1.04), respectively. The Health-conscious group was associated with lower levels of inflammatory biomarkers (e.g., C-reactive Protein) which are also known to be elevated in those with common metabolic diseases (e.g., cardiovascular disease). Other markers modulated in the Health-conscious group, ketone bodies, insulin-like growth factor-binding protein (IGFBP), and Growth Hormone 1 were more abundant, while leptin was less abundant. Further, the IGFBP pathway, which influences IGF1 activity, may be significantly enhanced by dietary choices.
CONCLUSIONS: These observations align with previous findings from studies focusing on weight loss interventions, which include a reduction in leptin levels. Overall, the Health-conscious group, with preference to healthier food options, has better health outcomes, compared to Sweet-tooth and Omnivore groups.}, }
@article {pmid39352141, year = {2024}, author = {Coclet, C and Camargo, AP and Roux, S}, title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.}, journal = {mSystems}, volume = {9}, number = {10}, pages = {e0088824}, pmid = {39352141}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Genome, Viral/genetics ; *Metagenomics/methods ; *Viruses/genetics/classification/isolation & purification ; Software ; Virome/genetics ; Computational Biology/methods ; Molecular Sequence Annotation ; }, abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.}, }
@article {pmid39352117, year = {2024}, author = {Gu, S and Shao, Y and Rehm, K and Bigler, L and Zhang, D and He, R and Xu, R and Shao, J and Jousset, A and Friman, VP and Bian, X and Wei, Z and Kümmerli, R and Li, Z}, title = {Feature sequence-based genome mining uncovers the hidden diversity of bacterial siderophore pathways.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39352117}, issn = {2050-084X}, support = {No. 2021YFF1200500//National Key Research and Development Program of China/ ; No. 42107140//National Natural Science Foundation of China/ ; No.41922053//National Natural Science Foundation of China/ ; No. 32071255//National Natural Science Foundation of China/ ; No. T2321001//National Natural Science Foundation of China/ ; No. BX2021012//National Postdoctoral Program for Innovative Talents/ ; no. 310030_212266/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Siderophores/metabolism/genetics ; *Genome, Bacterial ; *Pseudomonas/genetics/metabolism ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Oligopeptides/metabolism/genetics ; Secondary Metabolism/genetics ; Iron/metabolism ; }, abstract = {Microbial secondary metabolites are a rich source for pharmaceutical discoveries and play crucial ecological functions. While tools exist to identify secondary metabolite clusters in genomes, precise sequence-to-function mapping remains challenging because neither function nor substrate specificity of biosynthesis enzymes can accurately be predicted. Here, we developed a knowledge-guided bioinformatic pipeline to solve these issues. We analyzed 1928 genomes of Pseudomonas bacteria and focused on iron-scavenging pyoverdines as model metabolites. Our pipeline predicted 188 chemically different pyoverdines with nearly 100% structural accuracy and the presence of 94 distinct receptor groups required for the uptake of iron-loaded pyoverdines. Our pipeline unveils an enormous yet overlooked diversity of siderophores (151 new structures) and receptors (91 new groups). Our approach, combining feature sequence with phylogenetic approaches, is extendable to other metabolites and microbial genera, and thus emerges as powerful tool to reconstruct bacterial secondary metabolism pathways based on sequence data.}, }
@article {pmid39351379, year = {2024}, author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA}, title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.}, journal = {ERJ open research}, volume = {10}, number = {5}, pages = {}, pmid = {39351379}, issn = {2312-0541}, abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.
METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.
FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean±sd change -0.12±0.22 versus -0.11±0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109 318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.
INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.}, }
@article {pmid39351031, year = {2024}, author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D}, title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1379094}, pmid = {39351031}, issn = {2296-2565}, mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; }, abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.
METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.
RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.
DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.}, }
@article {pmid39349447, year = {2024}, author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q}, title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8469}, pmid = {39349447}, issn = {2041-1723}, mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs & derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; }, abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.}, }
@article {pmid39346055, year = {2024}, author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M}, title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17893}, pmid = {39346055}, issn = {2167-8359}, mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation & purification/classification ; Plants/microbiology ; Computational Biology/methods ; }, abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.}, }
@article {pmid39345378, year = {2024}, author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Gonzalez, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Bayabyan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, G and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, A and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Wagner, J and Xiao, C and Liss, AS and Zook, JM}, title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39345378}, issn = {2692-8205}, support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2 OD034190/OD/NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; }, abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from thirteen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, and Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic mutations. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.}, }
@article {pmid39345343, year = {2024}, author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and , and , and , and , }, title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {404}, pmid = {39345343}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.}, }
@article {pmid39343505, year = {2024}, author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ}, title = {Metabolic and Bariatric Surgery for Adolescents.}, journal = {Pediatric clinics of North America}, volume = {71}, number = {5}, pages = {981-998}, doi = {10.1016/j.pcl.2024.06.007}, pmid = {39343505}, issn = {1557-8240}, mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; }, abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.}, }
@article {pmid39341239, year = {2024}, author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH}, title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176491}, doi = {10.1016/j.scitotenv.2024.176491}, pmid = {39341239}, issn = {1879-1026}, abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.}, }
@article {pmid39340701, year = {2024}, author = {Gang, J and Ping, Y and Du, C}, title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {379}, pmid = {39340701}, issn = {1432-0991}, support = {32172468//National Natural Science Foundation of China/ ; }, mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; }, abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.}, }
@article {pmid39337302, year = {2024}, author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F}, title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.}, journal = {International journal of molecular sciences}, volume = {25}, number = {18}, pages = {}, pmid = {39337302}, issn = {1422-0067}, mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; }, abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.}, }
@article {pmid39332349, year = {2024}, author = {Sun, Q and Zhang, Z and Ping, Q and Wang, L and Li, Y}, title = {Insight into using multi-omics analysis to elucidate nitrogen removal mechanisms in a novel improved constructed rapid infiltration system: Functional gene and metabolite signatures.}, journal = {Water research}, volume = {267}, number = {}, pages = {122502}, doi = {10.1016/j.watres.2024.122502}, pmid = {39332349}, issn = {1879-2448}, mesh = {*Nitrogen/metabolism ; *Wastewater/chemistry ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrification ; Metabolomics ; Metagenomics ; Ammonium Compounds/metabolism ; Multiomics ; }, abstract = {In this study, a laboratory-scale improved constructed rapid infiltration (imCRI) system with non-saturated and saturated layers was constructed, and corn cobs as solid carbon source were added to the saturated layer to enhance the removal of nitrogen. Combined analyses of metagenomics and metabolomics were conducted to elucidate the nitrogen removal mechanism in the imCRI system. The results showed that the hydraulic load significantly influenced the treatment performance of the imCRI system, and a hydraulic load of 1.25 m[3]/(m[2]⋅d) was recommended. Under optimal conditions, the imCRI system using simulated wastewater achieved average removal efficiencies of 97.8 % for chemical oxygen demand, 85.7 % for total nitrogen (TN), and 97.6 % for ammonia nitrogen. Metagenomic and metabolomic analyses revealed that besides nitrification and denitrification, dissimilatory nitrate reduction to ammonium (DNRA), anammox, etc., are also involved in nitrogen metabolism in the imCRI system. Although nitrification was the predominant pathway in the non-saturated layer, aerobic denitrification also occurred, accounting for 22.59 % of the TN removal. In the saturated layer, nitrogen removal was attributed to synergistic effects of denitrification, DNRA and anammox. Moreover, correlation analysis among nitrogen removal, functional genes and metabolites suggested that metabolites related to the tricarboxylic acid cycle generated from the glycolysis of corn cobs provided sufficient energy for denitrification. Our results can offer a promising technology for decentralized wastewater treatment with stringent nitrogen removal requirements, and provide a foundation for understanding the underlying nitrogen transformation and removal mechanism.}, }
@article {pmid39331699, year = {2024}, author = {Yang, Z and Shan, Y and Liu, X and Chen, G and Pan, Y and Gou, Q and Zou, J and Chang, Z and Zeng, Q and Yang, C and Kong, J and Sun, Y and Li, S and Zhang, X and Wu, WC and Li, C and Peng, H and Holmes, EC and Guo, D and Shi, M}, title = {VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.}, journal = {Molecular biology and evolution}, volume = {41}, number = {10}, pages = {}, pmid = {39331699}, issn = {1537-1719}, support = {82341118//National Natural Science Foundation of China/ ; 2022A1515011854//Natural Science Foundation of Guangdong Province of China/ ; JCYJ20210324124414040//Shenzhen Science and Technology Program/ ; //Hong Kong Innovation and Technology Fund (ITF/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC (Australia) Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; }, mesh = {*RNA Viruses/genetics ; *Software ; *Metagenomics/methods ; *Phylogeny ; Humans ; RNA-Dependent RNA Polymerase/genetics ; Computational Biology/methods ; }, abstract = {RNA viruses exhibit vast phylogenetic diversity and can significantly impact public health and agriculture. However, current bioinformatics tools for viral discovery from metagenomic data frequently generate false positive virus results, overestimate viral diversity, and misclassify virus sequences. Additionally, current tools often fail to determine virus-host associations, which hampers investigation of the potential threat posed by a newly detected virus. To address these issues we developed VirID, a software tool specifically designed for the discovery and characterization of RNA viruses from metagenomic data. The basis of VirID is a comprehensive RNA-dependent RNA polymerase database to enhance a workflow that includes RNA virus discovery, phylogenetic analysis, and phylogeny-based virus characterization. Benchmark tests on a simulated data set demonstrated that VirID had high accuracy in profiling viruses and estimating viral richness. In evaluations with real-world samples, VirID was able to identify RNA viruses of all types, but also provided accurate estimations of viral genetic diversity and virus classification, as well as comprehensive insights into virus associations with humans, animals, and plants. VirID therefore offers a robust tool for virus discovery and serves as a valuable resource in basic virological studies, pathogen surveillance, and early warning systems for infectious disease outbreaks.}, }
@article {pmid39331660, year = {2024}, author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S}, title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012482}, pmid = {39331660}, issn = {1553-7358}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Models, Biological ; Computational Biology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.}, }
@article {pmid39331576, year = {2024}, author = {Qiao, B and Wang, S and Hou, M and Chen, H and Zhou, Z and Xie, X and Pang, S and Yang, C and Yang, F and Zou, Q and Sun, S}, title = {Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, doi = {10.1093/bioinformatics/btae581}, pmid = {39331576}, issn = {1367-4811}, support = {62273086//National Natural Science Foundation of China/ ; }, mesh = {*Deep Learning ; *NLR Proteins/metabolism ; *Computational Biology/methods ; Algorithms ; }, abstract = {MOTIVATION: Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable of detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs and effectors (CNE) determines the applicability and effectiveness of NLRs. Unfortunately, CNE data is very scarce. In fact, we've found a substantial 91 291 NLRs confirmed via wet experiments and bioinformatics methods but only 387 CNEs are recognized, which greatly restricts the potential application of NLRs.
RESULTS: We propose a deep learning algorithm called ProNEP to identify NLR-effector pairs in a high-throughput manner. Specifically, we conceptualized the CNE prediction task as a protein-protein interaction (PPI) prediction task. Then, ProNEP predicts the interaction between NLRs and effectors by combining the transfer learning with a bilinear attention network. ProNEP achieves superior performance against state-of-the-art models designed for PPI predictions. Based on ProNEP, we conduct extensive identification of potential CNEs for 91 291 NLRs. With the rapid accumulation of genomic data, we expect that this tool will be widely used to predict CNEs in new species, advancing biology, immunology, and breeding.
The ProNEP is available at http://nerrd.cn/#/prediction. The project code is available at https://github.com/QiaoYJYJ/ProNEP.}, }
@article {pmid39328967, year = {2024}, author = {Dey, B and Ferdous, J and Ahmed, R}, title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110908}, pmid = {39328967}, issn = {2352-3409}, abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.}, }
@article {pmid39326744, year = {2024}, author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T}, title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.}, journal = {The Science of the total environment}, volume = {954}, number = {}, pages = {176490}, doi = {10.1016/j.scitotenv.2024.176490}, pmid = {39326744}, issn = {1879-1026}, mesh = {*Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Crops, Agricultural ; *Machine Learning ; Environmental Monitoring/methods ; Soil/chemistry ; Environmental Pollution/statistics & numerical data ; }, abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial consequences of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.}, }
@article {pmid39326182, year = {2024}, author = {Li, D and Ping, Q and Mo, R and Guo, W and Zhang, S and Wang, L and Li, Y}, title = {Revealing synergistic mechanisms of biochar-assisted microbial electrolysis cells in enhancing the anaerobic digestion performance of waste activated sludge: Extracellular polymeric substances characterization, enzyme activity assay, and multi-omics analysis.}, journal = {Water research}, volume = {267}, number = {}, pages = {122501}, doi = {10.1016/j.watres.2024.122501}, pmid = {39326182}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Anaerobiosis ; *Extracellular Polymeric Substance Matrix/metabolism ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Electrolysis ; Methane/metabolism ; Multiomics ; }, abstract = {Although biochar (BC)-assisted microbial electrolysis cells (MEC) has been shown to improve anaerobic digestion (AD) performance of waste activated sludge (WAS), the underlying mechanisms remain unclear. This study conducted an in-depth investigation into the mechanism based on analyses of extracellular polymeric substances (EPS) characteristics, enzyme activities and multi-omics. The results showed that compared with the control group, methane production improved by 16.73 %, 21.32 %, and 29.37 % in the BC, MEC, and BC-assisted MEC (BC-MEC) groups, respectively. The reconfiguration of the protein secondary structure increased the hydrophobicity of the EPS, thereby promoting microbial aggregation. In addition, partial least-squares path modeling (PLS-PM) and mantel test based on the enzyme activity and multi-omics analyses revealed that the promotional effect of MEC on the hydrolysis of WAS was superior to that of BC, while BC was more advantageous in promoting electron transfer and biofilm formation regulated by quorum sensing. The synergistic effects of BC and MEC were exemplified in the BC-MEC group. g_norank_Aminicenantales responsible for the hydrolysis of WAS was enriched (29.6 %), and the activities of hydrolytic enzymes including α-glucosidases and proteases were increased by 29.1 % and 43.6 %, respectively. Further, the expressions of genes related to acyl homoserine lactones (AHLs) and diffusible signal factor (DSF) in quorum sensing systems, as well as the genes related to hydrogenase involved in electron transfer (mbhJKL, hyfB-JR, hypA-F, and hoxFHUY), were up-regulated in the BC-MEC group. This facilitated electron transfer and microbial communication, consequently enhancing methane production. This research significantly advances the understanding of the mechanism by which BC-assisted MEC enhances AD performance and provides valuable insights into strategies for improving energy recovery from WAS.}, }
@article {pmid39325874, year = {2024}, author = {Zhu, Y and Chen, G and Sun, Y}, title = {VirTAXA: enhancing RNA virus taxonomic classification with remote homology search and tree-based validation.}, journal = {Bioinformatics (Oxford, England)}, volume = {40}, number = {10}, pages = {}, pmid = {39325874}, issn = {1367-4811}, support = {11206819//City University of Hong Kong, Hong Kong Research Grants Council/ ; //Hong Kong Innovation and Technology Fund/ ; }, mesh = {*RNA Viruses/genetics/classification ; *Software ; RNA, Viral/genetics ; Phylogeny ; Sequence Analysis, RNA/methods ; Genome, Viral ; Algorithms ; Computational Biology/methods ; }, abstract = {SUMMARY: RNA viruses are ubiquitous across a broad spectrum of ecosystems. Therefore, beyond their significant implications for public health, RNA viruses are also key players in ecological processes. High-through sequencing has accelerated the discovery of RNA viruses. Nevertheless, many of these viruses lack taxonomic annotation, posing a challenge to functional inference and evolutionary study. In particular, virus classification at the genus level remains difficult due to the limited reference data and ambiguous boundaries between some closely related genera. We introduce VirTAXA, a robust classification tool that combines remote homology search and tree-based validation to enhance the genus-level taxonomic classification of RNA viruses. VirTAXA is able to predict the genus label of an assembled viral contig and provide evidence type for each prediction. It achieves comparable accuracy to state-of-the-art methods while assigning genus labels to a greater number of sequences. Specifically, on the Global Ocean RNA metatranscriptomic data, VirTAXA can assign genus labels for 18% more contigs than the second-best classification tool. Furthermore, we demonstrated that VirTAXA can be conveniently extended to other types of viruses.
The source code and data of VirTAXA are available via https://github.com/JudithEllyn/VirTAXA.}, }
@article {pmid39323974, year = {2022}, author = {Boyes, D and Crowley, LM and , and , and , and , and , and Skojec, C and Plotkin, D and Kawahara, AY and , }, title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {7}, number = {}, pages = {197}, pmid = {39323974}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.}, }
@article {pmid39323166, year = {2024}, author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR}, title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {9}, pages = {5494-5505}, doi = {10.13227/j.hjkx.202307274}, pmid = {39323166}, issn = {0250-3301}, abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.}, }
@article {pmid39321538, year = {2024}, author = {Cao, J and Lei, Y and Li, W and Jiang, X and Li, M}, title = {Coupled digital visualization and multi-omics uncover neurobehavioral dysfunction in zebrafish induced by resorcinol bis(diphenylphosphate).}, journal = {Environment international}, volume = {192}, number = {}, pages = {109023}, doi = {10.1016/j.envint.2024.109023}, pmid = {39321538}, issn = {1873-6750}, mesh = {Animals ; *Zebrafish/physiology ; Water Pollutants, Chemical/toxicity ; Blood-Brain Barrier/drug effects ; Resorcinols/toxicity ; Brain/drug effects/metabolism ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {Resorcinol bis(diphenylphosphate) (RDP) is an emerging pollutant that has been frequently detected in aquatic environments, although its toxicity is poorly characterized. To understand how RDP affects the neural system, two-month-old zebrafish were exposed to RDP at concentrations of 0.1 and 10 μg/L for 60 days. Following exposure, behavioral assessments were conducted, revealing the emergence of anxiety-like symptoms and memory deficits among the adult fish exposed to RDP, especially at the higher concentration. The increased blood-brain barrier (BBB) permeability (4.67-5.58-fold higher than the control group), reduced expression of tight junction proteins and the rapid brain RDP bioaccumulation (15.63 ± 2.34 ng/g wet weight) indicated the neurotoxicity of RDP. Excess reactive oxygen species synthesis (2.20-2.50-fold) was induced by RDP, leading to mitochondrial dysfunction and decreased production of neurotransmitters in the brain, specifically serotonin (5-HT; 16.3 %) and dopamine (DA; 18.1 %). Metabolomic analysis revealed that the low-toxicity RDP dose up-regulated lipid-related metabolites, while the high-toxicity dose up-regulated arachidonic acid metabolism and disrupted amino acid metabolism, including tryptophan and tyrosine metabolism related to dopaminergic and serotonergic pathways. The dysregulation of genes in various cellular processes was identified by transcriptomics, mainly involved in cell adhesion molecules and gap junctions, and oxidative phosphorylation, which were directly associated with BBB permeability and oxidative stress, respectively. Correlation analysis of microbiome-metabolite-host links built a mechanistic hypothesis for alterations in gut microbiota (Actinobacteriota and Proteobacteria) induced by high-dose RDP leading to the alteration of tryptophan, tyrosine, and arachidonic acid metabolism, decreasing the production of 5-HT and DA through the gut-brain axis. This study provides valuable insights into the mechanism underlying RDP-induced neurotoxicity in zebrafish, which can inform ecological risk assessments.}, }
@article {pmid39320588, year = {2024}, author = {Oroud, IM}, title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {979}, pmid = {39320588}, issn = {1573-2959}, mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; }, abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.}, }
@article {pmid39313745, year = {2024}, author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T}, title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.}, journal = {Nature aging}, volume = {4}, number = {10}, pages = {1493-1507}, pmid = {39313745}, issn = {2662-8465}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation ; CpG Islands/genetics ; Genome-Wide Association Study ; Aged ; Female ; Male ; Middle Aged ; Models, Statistical ; }, abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.}, }
@article {pmid39312537, year = {2024}, author = {Malamud, J and Guloksuz, S and van Winkel, R and Delespaul, P and De Hert, MAF and Derom, C and Thiery, E and Jacobs, N and Rutten, BPF and Huys, QJM}, title = {Characterizing the dynamics, reactivity and controllability of moods in depression with a Kalman filter.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012457}, pmid = {39312537}, issn = {1553-7358}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Affect/physiology ; *Depression/physiopathology ; *Computational Biology ; Algorithms ; Ecological Momentary Assessment ; Psychometrics/methods ; Male ; Female ; }, abstract = {BACKGROUND: Mood disorders involve a complex interplay between multifaceted internal emotional states, and complex external inputs. Dynamical systems theory suggests that this interplay between aspects of moods and environmental stimuli may hence determine key psychopathological features of mood disorders, including the stability of mood states, the response to external inputs, how controllable mood states are, and what interventions are most likely to be effective. However, a comprehensive computational approach to all these aspects has not yet been undertaken.
METHODS: Here, we argue that the combination of ecological momentary assessments (EMA) with a well-established dynamical systems framework-the humble Kalman filter-enables a comprehensive account of all these aspects. We first introduce the key features of the Kalman filter and optimal control theory and their relationship to aspects of psychopathology. We then examine the psychometric and inferential properties of combining EMA data with Kalman filtering across realistic scenarios. Finally, we apply the Kalman filter to a series of EMA datasets comprising over 700 participants with and without symptoms of depression.
RESULTS: The results show a naive Kalman filter approach performs favourably compared to the standard vector autoregressive approach frequently employed, capturing key aspects of the data better. Furthermore, it suggests that the depressed state involves alterations to interactions between moods; alterations to how moods responds to external inputs; and as a result an alteration in how controllable mood states are. We replicate these findings qualitatively across datasets and explore an extension to optimal control theory to guide therapeutic interventions.
CONCLUSIONS: Mood dynamics are richly and profoundly altered in depressed states. The humble Kalman filter is a well-established, rich framework to characterise mood dynamics. Its application to EMA data is valid; straightforward; and likely to result in substantial novel insights both into mechanisms and treatments.}, }
@article {pmid39309423, year = {2023}, author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , }, title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {529}, pmid = {39309423}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.}, }
@article {pmid39309224, year = {2024}, author = {Boyes, D and Lees, DC and Wawman, DC and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis & Schiffermüller) 1775.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {271}, pmid = {39309224}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.}, }
@article {pmid39309222, year = {2024}, author = {Boyes, D and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {348}, pmid = {39309222}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.28 kilobases in length.}, }
@article {pmid39304543, year = {2024}, author = {Hossen, MF and Sultana, N}, title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {10}, pages = {964}, pmid = {39304543}, issn = {1573-2959}, mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; }, abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.}, }
@article {pmid39303692, year = {2024}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {Cell}, volume = {187}, number = {19}, pages = {5468-5482.e11}, pmid = {39303692}, issn = {1097-4172}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation & purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.}, }
@article {pmid39301440, year = {2024}, author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , }, title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton & E. Newton, 1876).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {378}, pmid = {39301440}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.}, }
@article {pmid39295890, year = {2023}, author = {Boyes, D and Januszczak, I and , and , and , and , and , and , }, title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {545}, pmid = {39295890}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.}, }
@article {pmid39294496, year = {2024}, author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A}, title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.}, journal = {Nature genetics}, volume = {56}, number = {11}, pages = {2455-2465}, pmid = {39294496}, issn = {1546-1718}, mesh = {Humans ; *Tumor Microenvironment/genetics ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; *Transcriptome ; *Neoplasm Metastasis/genetics ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling/methods ; Female ; }, abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.}, }
@article {pmid39292721, year = {2024}, author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB}, title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011649}, pmid = {39292721}, issn = {1553-7358}, mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; }, abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.}, }
@article {pmid39292164, year = {2024}, author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K}, title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.}, journal = {Scandinavian journal of work, environment & health}, volume = {50}, number = {7}, pages = {567-576}, pmid = {39292164}, issn = {1795-990X}, support = {240801-01//Industrial Disease Clinical Research Grants from the Ministry of Health, Labor and Welfare/ ; }, mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; }, abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.
METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.
RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.
CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.}, }
@article {pmid39292040, year = {2024}, author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC}, title = {Underreporting of violence against women: an analysis of two data sources.}, journal = {Ciencia & saude coletiva}, volume = {29}, number = {10}, pages = {e07732023}, doi = {10.1590/1413-812320242910.07732023}, pmid = {39292040}, issn = {1678-4561}, mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics & numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics & numerical data ; Information Systems/statistics & numerical data ; Information Sources ; }, abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.}, }
@article {pmid39290666, year = {2024}, author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW}, title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70233}, pmid = {39290666}, issn = {2045-7758}, abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.}, }
@article {pmid39290433, year = {2024}, author = {Castrillo, M and Aguilar, F and García-Díaz, D}, title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110839}, pmid = {39290433}, issn = {2352-3409}, abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.}, }
@article {pmid39290364, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {88}, pmid = {39290364}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.}, }
@article {pmid39290036, year = {2024}, author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D}, title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.}, journal = {Pharmacoepidemiology and drug safety}, volume = {33}, number = {9}, pages = {e70004}, doi = {10.1002/pds.70004}, pmid = {39290036}, issn = {1099-1557}, support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; }, mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration & dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics & numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; }, abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.
METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.
RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100 000 inhabitants and day) and incidence. The DID was 70% less than expected 12 months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.
CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.}, }
@article {pmid39289538, year = {2024}, author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ}, title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.}, journal = {npj biodiversity}, volume = {3}, number = {1}, pages = {28}, pmid = {39289538}, issn = {2731-4243}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.}, }
@article {pmid39287883, year = {2024}, author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR}, title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.}, journal = {Bulletin of mathematical biology}, volume = {86}, number = {11}, pages = {128}, pmid = {39287883}, issn = {1522-9602}, support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; }, abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.}, }
@article {pmid39287032, year = {2024}, author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H}, title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.}, journal = {Journal of wound care}, volume = {33}, number = {9}, pages = {678-686}, doi = {10.12968/jowc.2024.0189}, pmid = {39287032}, issn = {0969-0700}, mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics & numerical data ; Treatment Outcome ; Health Care Costs/statistics & numerical data ; }, abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.
METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.
RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (€2099) by 23.7% compared with dressings without TLC-NOSF (€2751) (p<0.001), as well as the resources used.
CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.}, }
@article {pmid39283951, year = {2024}, author = {Amaral, AS and Devos, DP}, title = {The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012459}, pmid = {39283951}, issn = {1553-7358}, mesh = {*Proteome/metabolism ; Databases, Protein ; Computational Biology ; Proteins/metabolism/chemistry ; Humans ; Proteomics/methods ; Bacteria/metabolism/genetics ; Animals ; }, abstract = {An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.}, }
@article {pmid39283104, year = {2024}, author = {Tedim, AP and Almeida-Santos, AC and Lanza, VF and Novais, C and Coque, TM and Freitas, AR and Peixe, L and , }, title = {Bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis: bioinformatic analysis using a tailored genomics framework.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {10}, pages = {e0137624}, pmid = {39283104}, issn = {1098-5336}, support = {EXPL/SAU-INF/0261/2021, UIDP/04378/2020, UIDB/04378/2020, LA/P/0140/2020, UI/BD/151317/2021//MCTES | Fundação para a Ciência e a Tecnologia (FCT)/ ; }, mesh = {*Bacteriocins/genetics/metabolism ; *Enterococcus faecium/genetics/metabolism/drug effects ; *Genomics ; *Computational Biology ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; Enterococcus/genetics/metabolism/drug effects ; }, abstract = {UNLABELLED: Multidrug-resistant Enterococcus faecium strains represent a major concern due to their ability to thrive in diverse environments and cause life-threatening infections. While antimicrobial resistance and virulence mechanisms have been extensively studied, the contribution of bacteriocins to E. faecium's adaptability remains poorly explored. E. faecium, within the Bacillota phylum, is a prominent bacteriocin producer. Here, we developed a tailored database of 76 Bacillota bacteriocins (217 sequences, including 40 novel bacteriocins) and applied it to uncover bacteriocin distribution patterns in 997 quality-filtered E. faecium and Enterococcus lactis (former E. faecium clade B) genomes. Curated using computational pipelines and literature mining, our database demonstrates superior precision versus leading public tools in identifying diverse bacteriocins. Distinct bacteriocin profiles emerged between E. faecium and E. lactis, highlighting species-specific adaptations. E. faecium strains from hospitalized patients were significantly enriched in bacteriocins as enterocin A and bacteriocins 43 (or T8), AS5, and AS11. These bacteriocin genes were strongly associated with antibiotic resistance, particularly vancomycin and ampicillin, and Inc18 rep2_pRE25-derivative plasmids, classically associated with vancomycin resistance transposons. Such bacteriocin arsenal likely enhances the adaptability and competitive fitness of E. faecium in the nosocomial environment. By combining a novel tailored database, whole-genome sequencing, and epidemiological data, our work elucidates meaningful connections between bacteriocin determinants, antimicrobial resistance, mobile genetic elements, and ecological origins in E. faecium and provides a framework for elucidating bacteriocin landscapes in other organisms. Characterizing species- and strain-level differences in bacteriocin profiles may reveal determinants of ecological adaptation, and translating these discoveries could further inform strategies to exploit bacteriocins against high-risk clones.
IMPORTANCE: This work significantly expands the knowledge on the understudied bacteriocin diversity in opportunistic enterococci, revealing their contribution in the adaptation to different environments. It underscores the importance of placing increased emphasis on genetic platforms carrying bacteriocins as well as on cryptic plasmids that often exclusively harbor bacteriocins since bacteriocin production can significantly contribute to plasmid maintenance, potentially facilitating their stable transmission across generations. Further characterization of strain-level bacteriocin landscapes could inform strategies to combat high-risk clones. Overall, these insights provide a framework for unraveling the therapeutic and biotechnological potential of bacteriocins.}, }
@article {pmid39277496, year = {2024}, author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A}, title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].}, journal = {General hospital psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.genhosppsych.2024.09.006}, pmid = {39277496}, issn = {1873-7714}, }
@article {pmid39275913, year = {2024}, author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T}, title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.}, journal = {FEBS open bio}, volume = {14}, number = {12}, pages = {1972-1984}, pmid = {39275913}, issn = {2211-5463}, support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Japan ; *Gastrointestinal Microbiome/genetics ; *Birds/microbiology/virology ; *Metagenomics/methods ; Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; }, abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.}, }
@article {pmid39274728, year = {2024}, author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M}, title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.}, journal = {Materials (Basel, Switzerland)}, volume = {17}, number = {17}, pages = {}, pmid = {39274728}, issn = {1996-1944}, abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.}, }
@article {pmid39273837, year = {2024}, author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A}, title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {17}, pages = {}, pmid = {39273837}, issn = {2223-7747}, abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.}, }
@article {pmid39273245, year = {2024}, author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI}, title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.}, journal = {International journal of molecular sciences}, volume = {25}, number = {17}, pages = {}, pmid = {39273245}, issn = {1422-0067}, support = {23-15-00113//Russian Science Foundation/ ; }, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; }, abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.}, }
@article {pmid39271937, year = {2024}, author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D}, title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.}, journal = {Nature ecology & evolution}, volume = {8}, number = {12}, pages = {2336}, doi = {10.1038/s41559-024-02557-8}, pmid = {39271937}, issn = {2397-334X}, }
@article {pmid39271747, year = {2024}, author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H}, title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21377}, pmid = {39271747}, issn = {2045-2322}, support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; }, mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; }, abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.}, }
@article {pmid39269993, year = {2024}, author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T}, title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011609}, pmid = {39269993}, issn = {1553-7358}, mesh = {Animals ; Humans ; *Malaria/transmission/prevention & control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; }, abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.}, }
@article {pmid39269992, year = {2024}, author = {O'Meara, BC and Beaulieu, JM}, title = {Noise leads to the perceived increase in evolutionary rates over short time scales.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012458}, pmid = {39269992}, issn = {1553-7358}, mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; }, abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.}, }
@article {pmid39267994, year = {2024}, author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {258}, pmid = {39267994}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.}, }
@article {pmid39266599, year = {2024}, author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C}, title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {21288}, pmid = {39266599}, issn = {2045-2322}, support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; }, abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.}, }
@article {pmid39264951, year = {2024}, author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB}, title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012445}, pmid = {39264951}, issn = {1553-7358}, mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; }, abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.}, }
@article {pmid39264914, year = {2024}, author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F}, title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0308013}, pmid = {39264914}, issn = {1932-6203}, mesh = {*Flowers/genetics/metabolism/growth & development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; }, abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.}, }
@article {pmid39264239, year = {2024}, author = {Silva, M and Capps, S and London, JK}, title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.}, journal = {Birth defects research}, volume = {116}, number = {9}, pages = {e2395}, pmid = {39264239}, issn = {2472-1727}, support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; }, abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).
METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.
RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.
CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.}, }
@article {pmid39263387, year = {2024}, author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA}, title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e129438}, pmid = {39263387}, issn = {1314-2828}, abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.
NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb & Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam & Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Prószyński & Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaBösenberg & Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam & Benjamin, 2019 andProszynskiaKanesharatnam & Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam & Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(Bösenberg & Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.}, }
@article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, ÅJ and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.
METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.
RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.
CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, }
@article {pmid39257810, year = {2024}, author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ}, title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39257810}, issn = {2692-8205}, support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; }, abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.}, }
@article {pmid39257624, year = {2024}, author = {Lohse, K and Vila, R and Hayward, A and , and , and , and , and , }, title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {266}, pmid = {39257624}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.}, }
@article {pmid39257623, year = {2024}, author = {Boyes, D and Januszczak, I and Lees, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {96}, pmid = {39257623}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.}, }
@article {pmid39257281, year = {2024}, author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S}, title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.}, journal = {Journal of the Royal Society, Interface}, volume = {21}, number = {218}, pages = {20240301}, pmid = {39257281}, issn = {1742-5662}, support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium für Bildung und Forschung/ ; //Sächsisches Staatsministerium für Wissenschaft und Kunst/ ; }, mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention & control ; }, abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.}, }
@article {pmid39255632, year = {2024}, author = {Amenu, K and Daborn, C and Huntington, B and Knight-Jones, T and Rushton, J and Grace, D}, title = {Prioritization, resource allocation and utilization of decision support tools in animal health: Results of qualitative interviews with experts.}, journal = {Preventive veterinary medicine}, volume = {233}, number = {}, pages = {106333}, doi = {10.1016/j.prevetmed.2024.106333}, pmid = {39255632}, issn = {1873-1716}, mesh = {Animals ; *Resource Allocation ; Decision Support Techniques ; Health Priorities ; Decision Making ; Animal Husbandry/methods ; Surveys and Questionnaires ; }, abstract = {A follow up to an online questionnaire survey (in a kind of a sequential study design), qualitative assessment was made on the views of selected animal health experts on disease prioritization methods, resource allocation and use of decision-support tools. This was done through in-depth interviews with experts working for national or international organizations and sectors. A semi-structured question guide was formulated based on the information generated in the online questionnaire and a systematic content analysis of animal and human health manuals for disease prioritization and resource allocation. In-depth, one-on-one, online interviews on the process of disease prioritization, animal health decision-making, types of prioritization tools and aspects of improvements in the tools were conducted during March and April 2022 with 20 expert informants. Prioritization approaches reported by experts were either single criterion-based or multiple criteria-based. Experts appreciated the single-criterion-based approach (quantitative) for its objectivity in contrast to multicriteria prioritization approaches which were criticized for their subjectivity. Interviews with the experts revealed a perceived lack of quality and reliable data to inform disease prioritization, especially in smallholder livestock production systems. It was found that outputs of disease prioritization exercises do not generally directly influence resource allocation in animal health and highlighted the paucity of funding for animal health compared to other agricultural sectors. The experts considered that the available decision-support tools in animal health need improvement in terms of data visualization for interpretation, management decision making and advocacy. Further recommendations include minimizing subjective biases by increasing the availability and quality of data and improving the translation of disease prioritization outputs into actions and the resources to deliver those actions. DATA AVAILABILITY STATEMENT: The data can be obtained from the corresponding author upon request.}, }
@article {pmid39255272, year = {2024}, author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF}, title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1012435}, pmid = {39255272}, issn = {1553-7358}, mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; }, abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.}, }
@article {pmid39255143, year = {2024}, author = {Jiang, W and Windl, M and Tag, B and Sarsenbayeva, Z and Mayer, S}, title = {An Immersive and Interactive VR Dataset to Elicit Emotions.}, journal = {IEEE transactions on visualization and computer graphics}, volume = {30}, number = {11}, pages = {7343-7353}, doi = {10.1109/TVCG.2024.3456202}, pmid = {39255143}, issn = {1941-0506}, mesh = {Humans ; *Emotions/physiology ; *Virtual Reality ; Female ; Male ; *Computer Graphics ; Adult ; Young Adult ; User-Computer Interface ; Databases, Factual ; Video Recording ; }, abstract = {Images and videos are widely used to elicit emotions; however, their visual appeal differs from real-world experiences. With virtual reality becoming more realistic, immersive, and interactive, we envision virtual environments to elicit emotions effectively, rapidly, and with high ecological validity. This work presents the first interactive virtual reality dataset to elicit emotions. We created five interactive virtual environments based on corresponding validated 360° videos and validated their effectiveness with 160 participants. Our results show that our virtual environments successfully elicit targeted emotions. Compared with the existing methods using images or videos, our dataset allows virtual reality researchers and practitioners to integrate their designs effectively with emotion elicitation settings in an immersive and interactive way.}, }
@article {pmid39253482, year = {2024}, author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V}, title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.05.570296}, pmid = {39253482}, issn = {2692-8205}, abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.}, }
@article {pmid39250076, year = {2024}, author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A}, title = {Web of venom: exploration of big data resources in animal toxin research.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {39250076}, issn = {2047-217X}, support = {//European Cooperation in Science and Technology/ ; //Fundação para a Ciência e a Tecnologia/ ; }, mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; }, abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.}, }
@article {pmid39244927, year = {2024}, author = {Ibrahim, AS and Kuuire, V and Kepe, T}, title = {On mapping urban community resilience: Land use vulnerability, coping and adaptive strategies in Ghana.}, journal = {Journal of environmental management}, volume = {370}, number = {}, pages = {122426}, doi = {10.1016/j.jenvman.2024.122426}, pmid = {39244927}, issn = {1095-8630}, mesh = {Ghana ; *Floods ; Humans ; *Cities ; Climate Change ; Urban Population ; Geographic Information Systems ; }, abstract = {Cities across the globe are prioritizing resilience in the wake of increasing climate change-related disasters. About 44% of these disasters are floods and their manifestation in cities is more pronounced, threatening urban social, ecological, and economic systems. This study draws on community resilience and participatory GIS, to examine land use vulnerability to flooding and local coping and adaptive strategies to achieve resilience. Using Ghana as a case study, the results show that participatory mapping offers community resilience benefits by providing context to community resilience challenges and potentials, enabling a deeper understanding of socio-environmental coupling that contributes to flood vulnerability and builds on community adaptive strategies through harnessing local community knowledge. We identified that topography, poor drainage and road network, rainfall variability, residents' land use practices, and land use planning conundrum drive disparities in land use vulnerability to flooding. Participants underscored the necessity of critical urban infrastructure in facilitating community adaptability to floods. The findings indicate that socio-spatial inequities threaten urban community resilience, especially in increasingly cosmopolitan urban contexts, by putting the marginalized urban population in a more vulnerable position. We recommend the prioritization of recognitional equity in community resilience planning efforts to allow for the targeting of resilient interventions that reflect and respect social differentiation in the urban environment so that outcomes will not exacerbate or generate new urban socio-spatial inequalities.}, }
@article {pmid39242865, year = {2023}, author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M}, title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.}, journal = {Communications psychology}, volume = {1}, number = {1}, pages = {43}, pmid = {39242865}, issn = {2731-9121}, abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.}, }
@article {pmid39242702, year = {2023}, author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S}, title = {What drives our aesthetic attraction to birds?.}, journal = {npj biodiversity}, volume = {2}, number = {1}, pages = {20}, pmid = {39242702}, issn = {2731-4243}, abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.}, }
@article {pmid39240878, year = {2024}, author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD}, title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.}, journal = {PloS one}, volume = {19}, number = {9}, pages = {e0295662}, pmid = {39240878}, issn = {1932-6203}, mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; }, abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.}, }
@article {pmid39239169, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {104}, pmid = {39239169}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.}, }
@article {pmid39235751, year = {2025}, author = {Lemée, P and Bridier, A}, title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2852}, number = {}, pages = {289-309}, pmid = {39235751}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; }, abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.}, }
@article {pmid39233902, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {117}, pmid = {39233902}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.}, }
@article {pmid39233899, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {31}, pmid = {39233899}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.}, }
@article {pmid39233418, year = {2024}, author = {Li, X and Zhang, LY and Wu, C}, title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {7}, pages = {1887-1896}, doi = {10.13287/j.1001-9332.202407.021}, pmid = {39233418}, issn = {1001-9332}, mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; }, abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.}, }
@article {pmid39233286, year = {2024}, author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ}, title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.}, journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP}, volume = {286}, number = {}, pages = {110027}, doi = {10.1016/j.cbpc.2024.110027}, pmid = {39233286}, issn = {1532-0456}, mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; }, abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.}, }
@article {pmid39233066, year = {2024}, author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Luo, Y and Miao, L and Zhang, L and Li, J and Zhao, R}, title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.}, journal = {The Science of the total environment}, volume = {952}, number = {}, pages = {175996}, doi = {10.1016/j.scitotenv.2024.175996}, pmid = {39233066}, issn = {1879-1026}, abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.}, }
@article {pmid39230451, year = {2024}, author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E}, title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1912}, pages = {20220525}, pmid = {39230451}, issn = {1471-2970}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; }, abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.}, }
@article {pmid39229001, year = {2024}, author = {Obbard, DJ and , and , and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {365}, pmid = {39229001}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.}, }
@article {pmid39226337, year = {2024}, author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O}, title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.}, journal = {PLoS computational biology}, volume = {20}, number = {9}, pages = {e1011914}, pmid = {39226337}, issn = {1553-7358}, mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; }, abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.}, }
@article {pmid39225619, year = {2024}, author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B}, title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {11}, number = {41}, pages = {e2403393}, pmid = {39225619}, issn = {2198-3844}, support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; }, mesh = {Mice ; *Microbiota ; Animals ; *Neoplasms/microbiology ; *Neural Networks, Computer ; Humans ; Reproducibility of Results ; Disease Models, Animal ; }, abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.}, }
@article {pmid39224879, year = {2023}, author = {Boyes, D and Mulley, JF and , and , and , and , and , and , }, title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {441}, pmid = {39224879}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.}, }
@article {pmid39224768, year = {2024}, author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and , and , and , and , and , }, title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {189}, pmid = {39224768}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.}, }
@article {pmid39224703, year = {2024}, author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L}, title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1442062}, pmid = {39224703}, issn = {2235-2988}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention & control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention & control/microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.
METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.
RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.
DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.}, }
@article {pmid39222768, year = {2024}, author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I}, title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {361}, number = {}, pages = {124871}, doi = {10.1016/j.envpol.2024.124871}, pmid = {39222768}, issn = {1873-6424}, mesh = {Arctic Regions ; *Soil/chemistry ; Russia ; Environmental Monitoring/methods ; Soil Pollutants/analysis ; Thorium/analysis ; Cesium Radioisotopes/analysis ; Soil Pollutants, Radioactive/analysis ; Radiation Monitoring/methods ; Animals ; Birds ; Radioisotopes/analysis ; Radium ; }, abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.}, }
@article {pmid39222062, year = {2024}, author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I}, title = {CAIM: coverage-based analysis for identification of microbiome.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39222062}, issn = {1477-4054}, support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.}, }
@article {pmid39222055, year = {2024}, author = {Xu, C and Wang, JC and Sun, L and Zhuang, LH and Guo, ZJ and Ding, QS and Ma, DN and Song, LY and Li, J and Tang, HC and Zhu, XY and Zheng, HL}, title = {Genome-Wide Identification of Pentatricopeptide Repeat (PPR) Gene Family and Multi-Omics Analysis Provide New Insights Into the Albinism Mechanism of Kandelia obovata Propagule Leaves.}, journal = {Plant, cell & environment}, volume = {47}, number = {12}, pages = {5498-5510}, doi = {10.1111/pce.15132}, pmid = {39222055}, issn = {1365-3040}, support = {//This study was supported by the Natural Science Foundation of China (NSFC) (32171740, 31870581) and the National Key Research and Development Program of China (2017YFC0506102)./ ; }, mesh = {*Plant Leaves/genetics/metabolism ; *Genome-Wide Association Study ; *Plant Proteins/genetics/metabolism ; Multigene Family ; RNA Editing/genetics ; Rhizophoraceae/genetics/physiology ; Phylogeny ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; Genes, Plant ; Genome, Plant ; Multiomics ; }, abstract = {Pentatricopeptide repeat (PPR) gene family constitutes one of the largest gene families in plants, which mainly participate in RNA editing and RNA splicing of organellar RNAs, thereby affecting the organellar development. Recently, some evidence elucidated the important roles of PPR proteins in the albino process of plant leaves. However, the functions of PPR genes in the woody mangrove species have not been investigated. In this study, using a typical true mangrove Kandelia obovata, we systematically identified 298 PPR genes and characterized their general features and physicochemical properties, including evolutionary relationships, the subcellular localization, PPR motif type, the number of introns and PPR motifs, and isoelectric point, and so forth. Furthermore, we combined genome-wide association studies (GWAS) and transcriptome analysis to identify the genetic architecture and potential PPR genes associated with propagule leaves colour variations of K. obovata. As a result, we prioritized 16 PPR genes related to the albino phenotype using different strategies, including differentially expressed genes analysis and genetic diversity analysis. Further analysis discovered two genes of interest, namely Maker00002998 (PLS-type) and Maker00003187 (P-type), which were differentially expressed genes and causal genes detected by GWAS analysis. Moreover, we successfully predicted downstream target chloroplast genes (rps14, rpoC1 and rpoC2) bound by Maker00002998 PPR proteins. The experimental verification of RNA editing sites of rps14, rpoC1, and rpoC2 in our previous study and the verification of interaction between Maker00002998 and rps14 transcript using in vitro RNA pull-down assays revealed that Maker00002998 PPR protein might be involved in the post-transcriptional process of chloroplast genes. Our result provides new insights into the roles of PPR genes in the albinism mechanism of K. obovata propagule leaves.}, }
@article {pmid39221663, year = {2024}, author = {Crawford, AD and Slavin, R and Tabar, M and Radhakrishnan, K and Wang, M and Estrada, A and McGrath, JM}, title = {Methodological approaches in developing and implementing digital health interventions amongst underserved women.}, journal = {Public health nursing (Boston, Mass.)}, volume = {41}, number = {6}, pages = {1612-1621}, doi = {10.1111/phn.13410}, pmid = {39221663}, issn = {1525-1446}, mesh = {Humans ; Female ; *Telemedicine ; Texas ; Vulnerable Populations ; Women's Health ; Medically Underserved Area ; Artificial Intelligence ; Adult ; Mobile Applications ; Digital Health ; }, abstract = {BACKGROUND: Minority populations are utilizing mobile health applications more frequently to access health information. One group that may benefit from using mHealth technology is underserved women, specifically those on community supervision.
OBJECTIVE: Discuss methodological approaches for navigating digital health strategies to address underserved women's health disparities.
Using an intersectional lens, we identified strategies for conducting research using digital health technology and artificial intelligence amongst the underserved, particularly those with community supervision.
We explore (1) methodological approaches that combine traditional research methods with precision medicine, digital phenotyping, and ecological momentary assessment; (2) implications for artificial intelligence; and (3) ethical considerations with data collection, storage, and engagement.
DISCUSSION: Researchers must address gendered differences related to health, social, and economic disparities concurrently with an unwavering focus on the protection of human subjects when addressing the unique needs of underserved women while utilizing digital health methodologies.
PUBLIC CONTRIBUTION: Women on community supervision in South Central Texas helped inform the design of JUN, the mHealth app we reported in the case exemplar. JUN is named after the Junonia shell, a native shell to South Texas, which means strength, power, and self-sufficiency, like the participants in our preliminary studies.}, }
@article {pmid39221442, year = {2024}, author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , }, title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {312}, pmid = {39221442}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.}, }
@article {pmid39219129, year = {2024}, author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q}, title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.}, journal = {Water science and technology : a journal of the International Association on Water Pollution Research}, volume = {89}, number = {2}, pages = {252-270}, doi = {10.2166/wst.2023.413}, pmid = {39219129}, issn = {0273-1223}, mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; }, abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.}, }
@article {pmid39209912, year = {2024}, author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X}, title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {944}, pmid = {39209912}, issn = {2052-4463}, support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; }, abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.}, }
@article {pmid39209853, year = {2024}, author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H}, title = {Massive expansion of the pig gut virome based on global metagenomic mining.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {76}, pmid = {39209853}, issn = {2055-5008}, mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; }, abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.}, }
@article {pmid39213392, year = {2024}, author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J}, title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39213392}, issn = {1758-0463}, support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; }, mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; }, abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.}, }
@article {pmid39213378, year = {2024}, author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y}, title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.}, journal = {Molecular biology and evolution}, volume = {41}, number = {9}, pages = {}, pmid = {39213378}, issn = {1537-1719}, support = {//National Natural Science Foundation of China/ ; //National Key R&D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; }, mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; }, abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.}, }
@article {pmid39209112, year = {2024}, author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S}, title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: The Comprehensive National Nutrition Survey.}, journal = {The Journal of nutrition}, volume = {154}, number = {10}, pages = {2932-2947}, doi = {10.1016/j.tjnut.2024.08.021}, pmid = {39209112}, issn = {1541-6100}, mesh = {Humans ; India/epidemiology ; Adolescent ; Child ; Female ; Male ; Prevalence ; *Nutrition Surveys ; Child, Preschool ; *Malnutrition/epidemiology ; Nutritional Status ; Young Adult ; Overnutrition/epidemiology ; Socioeconomic Factors ; Child Nutrition Disorders/epidemiology ; }, abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health.
OBJECTIVES: This study aimed to examine the prevalence and correlates of double burden of malnutrition (DBM) and triple burden of malnutrition (TBM) among children and adolescents (5-19 y) to inform policies and programs.
METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any 2 forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all 3 forms of malnutrition. The prevalence of DBM, DBM+, and TBM was estimated accounting for probabilistic selection. We used mixed-effect binomial regression to determine correlates of DBM/TBM in children and adolescents separately.
RESULTS: The prevalence of DBM, DBM+, and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in girls compared to in boys in the 5-9 y age group. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling, and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.
CONCLUSIONS: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.}, }
@article {pmid39208288, year = {2024}, author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M}, title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.}, journal = {Evolution; international journal of organic evolution}, volume = {78}, number = {12}, pages = {1916-1935}, doi = {10.1093/evolut/qpae117}, pmid = {39208288}, issn = {1558-5646}, support = {MFFALIMN0001//The Max Planck Society/ ; 395940726//Magnetoreception and Navigation in Vertebrates/ ; 407495230//DFG Research Infrastructure/ ; 423957469//Next Generation Sequencing Competence Network/ ; 1ZIAHG200398//Intramural Research Program of the NHGRI/ ; //Spanish Ministry of Science/ ; //Innovation and Universities/ ; PGC2018-097575-B-I00//The European Regional Development Fund/ ; }, mesh = {Animals ; *Haplotypes ; *Recombination, Genetic ; *Genetic Variation ; *Songbirds/genetics ; Selection, Genetic ; Genome ; }, abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequencing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.}, }
@article {pmid39208193, year = {2024}, author = {Naser, AY}, title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0309362}, pmid = {39208193}, issn = {1932-6203}, mesh = {Humans ; *Hospitalization/statistics & numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; }, abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.
METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.
RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.
CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.}, }
@article {pmid39205176, year = {2024}, author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R}, title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.}, journal = {Viruses}, volume = {16}, number = {8}, pages = {}, pmid = {39205176}, issn = {1999-4915}, support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigué scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; }, mesh = {Animals ; *Culex/virology/growth & development ; *Aedes/virology/growth & development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth & development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; }, abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.}, }
@article {pmid39202353, year = {2024}, author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB}, title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.}, journal = {Genes}, volume = {15}, number = {8}, pages = {}, pmid = {39202353}, issn = {2073-4425}, support = {24-14-20015//the Russian Science Foundation/ ; }, mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; }, abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.}, }
@article {pmid39202178, year = {2024}, author = {de Llanza Varona, M and Martínez, M}, title = {Synergy Makes Direct Perception Inefficient.}, journal = {Entropy (Basel, Switzerland)}, volume = {26}, number = {8}, pages = {}, pmid = {39202178}, issn = {1099-4300}, support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovación y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; }, abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.}, }
@article {pmid39198944, year = {2024}, author = {Wang, HT and Li, HY and Lu, QW and He, SL}, title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].}, journal = {Se pu = Chinese journal of chromatography}, volume = {42}, number = {9}, pages = {856-865}, pmid = {39198944}, issn = {1872-2059}, mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; }, abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.}, }
@article {pmid39198489, year = {2024}, author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB}, title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19928}, pmid = {39198489}, issn = {2045-2322}, mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation & purification/pathogenicity ; Humans ; Livestock/microbiology ; }, abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.}, }
@article {pmid39198479, year = {2024}, author = {Zhu, J and Li, Z and Yang, J and Yu, K and Zhang, D and Zhong, J}, title = {Ecological space management and control zoning of Giant Panda National Park from the perspective of ecosystem services and land use.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {19951}, pmid = {39198479}, issn = {2045-2322}, support = {GJGY2020-ZD002//Key Project of National Park Research Center, Key Social Science Research Base of Sichuan Province, "National Park Natural Ecosystem Service Function Importance Evaluation and Protection Policy Research"/ ; ZDJS202303//Chengdu University of Technology "Double First-Class" initiative Construction Philosophy and Social Sciences Key Construction Project/ ; }, mesh = {Animals ; Bayes Theorem ; Carbon Sequestration ; China ; Computer Simulation ; *Conservation of Natural Resources/legislation & jurisprudence/methods ; Conservation of Water Resources ; Datasets as Topic ; *Ecosystem ; *Parks, Recreational/legislation & jurisprudence/organization & administration/standards ; Probability ; Soil ; *Ursidae ; Ecology/legislation & jurisprudence/methods/organization & administration ; }, abstract = {Since China proposed building a national park system in 2017, the establishment of a planning system for nature reserves, with national parks as the main body, is being actively promoted around the country. Among them, scientific ecological space management and control zoning (ESMCZ) is an important link in maintaining the ecological stability of national parks. How to zone national parks and how to improve the precision of zoning has become a new task for national parks. Therefore, this study takes the Giant Panda National Park as the study area, takes ecosystem services and land use/cover change as the research perspective, integrates the InVEST model, PLUS model and bayes belief network (BBN) model, and builds a set of ecological space management and control zoning (ESMCZ) spatial zoning framework based on raster scale, dividing the study area into strictly protected zone, ecological buffer zone, ecological control zone and controlled development zone. The results showed that: (1) The study area showed an increasing trend in water conservation, soil conservation and carbon storage from 2005 to 2020, and the habitat quality index was generally high. The spatial heterogeneity of ecosystem services in the study area was significant, and the effect of a single factor on ecosystem services was most pronounced. (2) Large variation in area for different land uses under natural development scenarios and ecological protection scenarios. In both scenarios, the area of cultivated land, the area of grassland and the area of unused land decrease relative to 2020, and the area of forested land, the area of water and the area of constructed land increase relative to 2020. (3) The Giant Panda National Park is divided into strictly protected zone, ecological buffer zone, ecological control zone and control development zone, of which the strictly protected zone have the largest area and the best ecosystem background condition, and the control development zone have the smallest area and the worst ecosystem background condition. (4) The ecological space management and control zoning (ESMCZ) framework provides a more refined method for the secondary zoning of nature reserves such as the Giant Panda National Park, which is valuable for the implementation of zoning and categorization management for ecological conservation in the Giant Panda National Park.}, }
@article {pmid39196880, year = {2024}, author = {Tsigeman, E and Zemliak, V and Likhanov, M and Papageorgiou, KA and Kovas, Y}, title = {AI can see you: Machiavellianism and extraversion are reflected in eye-movements.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0308631}, pmid = {39196880}, issn = {1932-6203}, mesh = {Humans ; *Eye Movements/physiology ; Male ; Female ; Adolescent ; *Extraversion, Psychological ; *Machine Learning ; *Machiavellianism ; Surveys and Questionnaires ; Algorithms ; Personality/physiology ; Eye-Tracking Technology ; }, abstract = {INTRODUCTION: Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms.
METHODS: Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron.
RESULTS AND DISCUSSION: Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.}, }
@article {pmid39193916, year = {2024}, author = {Spöri, Y and Flot, JF}, title = {Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39193916}, issn = {1477-4054}, support = {T.0078.23//Fonds de la Recherche Scientifique - FNRS/ ; }, mesh = {*Computational Biology/methods ; *Programming Languages ; *Software ; }, abstract = {Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.}, }
@article {pmid39193399, year = {2024}, author = {Boyes, D and Crowley, LM and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , }, title = {The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {200}, pmid = {39193399}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Noctua comes (the Lesser Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 540.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,001 protein coding genes.}, }
@article {pmid39193313, year = {2024}, author = {Kang, B and Ma, J and Jeong, I and Yoon, S and Kim, JI and Heo, SJ and Oh, SS}, title = {Behavioral marker-based predictive modeling of functional status for older adults with subjective cognitive decline and mild cognitive impairment: Study protocol.}, journal = {Digital health}, volume = {10}, number = {}, pages = {20552076241269555}, pmid = {39193313}, issn = {2055-2076}, abstract = {OBJECTIVE: This study describes a research protocol for a behavioral marker-based predictive model that examines the functional status of older adults with subjective cognitive decline and mild cognitive impairment.
METHODS: A total of 130 older adults aged ≥65 years with subjective cognitive decline or mild cognitive impairment will be recruited from the Dementia Relief Centers or the Community Service Centers. Data on behavioral and psychosocial markers (e.g. physical activity, mobility, sleep/wake patterns, social interaction, and mild behavioral impairment) will be collected using passive wearable actigraphy, in-person questionnaires, and smartphone-based ecological momentary assessments. Two follow-up assessments will be performed at 12 and 24 months after baseline. Mixed-effect machine learning models: MErf, MEgbm, MEmod, and MEctree, and standard machine learning models without random effects [random forest, gradient boosting machine] will be employed in our analyses to predict functional status over time.
RESULTS: The results of this study will be fundamental for developing tailored digital interventions that apply deep learning techniques to behavioral data to predict, identify, and aid in the management of functional decline in older adults with subjective cognitive decline and mild cognitive impairment. These older adults are considered the optimal target population for preventive interventions and will benefit from such tailored strategies.
CONCLUSIONS: Our study will contribute to the development of self-care interventions that utilize behavioral data and machine learning techniques to provide automated analyses of the functional decline of older adults who are at risk for dementia.}, }
@article {pmid39193090, year = {2023}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , }, title = {The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {509}, pmid = {39193090}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.}, }
@article {pmid39192185, year = {2024}, author = {Donthu, R and Marcelino, JAP and Giordano, R and Tao, Y and Weber, E and Avalos, A and Band, M and Akraiko, T and Chen, SC and Reyes, MP and Hao, H and Ortiz-Alvarado, Y and Cuff, CA and Claudio, EP and Soto-Adames, F and Smith-Pardo, AH and Meikle, WG and Evans, JD and Giray, T and Abdelkader, FB and Allsopp, M and Ball, D and Morgado, SB and Barjadze, S and Correa-Benitez, A and Chakir, A and Báez, DR and Chavez, NHM and Dalmon, A and Douglas, AB and Fraccica, C and Fernández-Marín, H and Galindo-Cardona, A and Guzman-Novoa, E and Horsburgh, R and Kence, M and Kilonzo, J and Kükrer, M and Le Conte, Y and Mazzeo, G and Mota, F and Muli, E and Oskay, D and Ruiz-Martínez, JA and Oliveri, E and Pichkhaia, I and Romane, A and Sanchez, CG and Sikombwa, E and Satta, A and Scannapieco, AA and Stanford, B and Soroker, V and Velarde, RA and Vercelli, M and Huang, Z}, title = {HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {278}, pmid = {39192185}, issn = {1471-2105}, support = {PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; USDA-APHIS #AP20PPQS & T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; USDA-APHIS #AP20PPQS & T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; NSF-OISE #1545803//National Science Foundation, United States of America/ ; }, mesh = {Bees/genetics/classification ; Animals ; *Polymorphism, Single Nucleotide/genetics ; Genomics/methods ; }, abstract = {BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.
RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.
CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.}, }
@article {pmid39188222, year = {2024}, author = {Koracevic, G and Stojanovic, M and Zdravkovic, M and Lovic, D and Simic, D and Mladenovic, K}, title = {Proposal of a Modified Classification of Hypertensive Crises: Urgency, Impending Emergency, and Emergency.}, journal = {Current vascular pharmacology}, volume = {22}, number = {3}, pages = {180-186}, pmid = {39188222}, issn = {1875-6212}, mesh = {Humans ; *Hypertension/diagnosis/physiopathology/drug therapy/classification ; *Antihypertensive Agents/therapeutic use/adverse effects ; Risk Assessment ; Risk Factors ; *Blood Pressure/drug effects ; *Emergencies ; Prognosis ; Predictive Value of Tests ; Decision Support Techniques ; Clinical Decision-Making ; Hypertensive Crisis ; }, abstract = {Systemic arterial hypertension (HTN) is the main cause of morbidity and mortality, and HTN crises contribute significantly to an unfavourable clinical course. For decades, HTN crises have been dichotomized into hypertensive emergency (HTN-E) and hypertensive urgency (HTN-U). The main difference between the two is the presence of acute hypertension-mediated organ damage (HMOD) - if HMOD is present, HTN crisis is HTN-E; if not, it is HTN-U. Patients with HTN-E are in a life-threatening situation. They are hospitalized and receive antihypertensive drugs intravenously (IV). On the other hand, patients with HTN-U are usually not hospitalized and receive their antihypertensives orally. We suggest a modification of the current risk stratification scheme for patients with HTN crises. The new category would be the intermediate risk group, more precisely the 'impending HTN-E' group, with a higher risk in comparison to HTN-U and a lower risk than HTN-E. 'Impending HMOD' means that HMOD has not occurred (yet), and the prognosis is, therefore, better than in patients with ongoing HMOD. There are three main reasons to classify patients as having impending HTN-E: excessively elevated BP, high-risk comorbidities, and ongoing bleeding/high bleeding risk. Their combinations are probable. This approach may enable us to prevent some HTNEs by avoiding acute HMOD using a timely blood pressure treatment. This treatment should be prompt but controlled.}, }
@article {pmid39186487, year = {2024}, author = {Raj, U and Banerjee, A and Ray, S and Bhattacharya, S}, title = {Structure of higher-order interactions in social-ecological networks through Q-analysis of their neighbourhood and clique complex.}, journal = {PloS one}, volume = {19}, number = {8}, pages = {e0306409}, pmid = {39186487}, issn = {1932-6203}, mesh = {*Ecosystem ; Humans ; Models, Theoretical ; Madagascar ; Algorithms ; Social Networking ; Social Support ; Agriculture ; }, abstract = {This paper studies higher-order interactions in social-ecological networks, which formally represent interactions within the social and ecological units of an ecosystem. Many real-world social ecosystems exhibit not only pairwise interactions but also higher-order interactions among their units. Therefore, the conventional graph-theoretic description of networks falls short of capturing these higher-order interactions due to the inherent limitations of the graph definition. In this work, a mathematical framework for capturing the higher-order interactions of a social-ecological system has been given by incorporating notions from combinatorial algebraic topology. In order to achieve this, two different simplicial complexes, the clique and the neighbourhood complex, have been constructed from a pairwise social-ecological network. As a case study, the Q-analysis and a structural study of the interactions in the rural agricultural system of southern Madagascar have been done at various structural levels denoted by q. The results obtained by calculating all the structural vectors for both simplicial complexes, along with exciting results about the participation of facets of the clique complex at different q-levels, have been discussed. This work also establishes significant theorems concerning the dimension of the neighbourhood complex and clique complex obtained from the parent pairwise network.}, }
@article {pmid39185327, year = {2024}, author = {Panyushkina, IP and Jull, AJT and Molnár, M and Varga, T and Kontul', I and Hantemirov, R and Kukarskih, V and Sljusarenko, I and Myglan, V and Livina, V}, title = {The timing of the ca-660 BCE Miyake solar-proton event constrained to between 664 and 663 BCE.}, journal = {Communications earth & environment}, volume = {5}, number = {1}, pages = {454}, pmid = {39185327}, issn = {2662-4435}, abstract = {Extreme solar energetic particle events, known as Miyake events, are rare phenomena observed by cosmogenic isotopes, with only six documented. The timing of the ca. 660 BCE Miyake event remains undefined until now. Here, we assign its occurrence to 664-663 BCE through new radiocarbon measurements in gymnosperm larch tree rings from arctic-alpine biomes (Yamal and Altai). Using a 22-box carbon cycle model and Bayesian statistics, we calculate the radiocarbon production rate during the event that is 3.2-4.8 times higher than the average solar modulation, and comparable to the 774-775 CE solar-proton event. The prolonged radiocarbon signature manifests a 12‰ rise over two years. The non-uniform signal in the tree rings is likely driven by the low rate of CO2 gas exchange between the trees and the ambient atmosphere, and the high residence time of radiocarbon in the post-event stratosphere. We caution about using the event's pronounced signature for precise single-year-dating.}, }
@article {pmid39184546, year = {2024}, author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A}, title = {Computational strategies for cross-species knowledge transfer and translational biomedicine.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39184546}, issn = {2331-8422}, support = {R01 OD011116/OD/NIH HHS/United States ; R35 GM128765/GM/NIGMS NIH HHS/United States ; }, abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.}, }
@article {pmid39181462, year = {2024}, author = {de Vries, P}, title = {ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143078}, doi = {10.1016/j.chemosphere.2024.143078}, pmid = {39181462}, issn = {1879-1298}, mesh = {*United States Environmental Protection Agency ; *Databases, Factual ; *Software ; United States ; Ecotoxicology/methods ; Risk Assessment/methods ; Reproducibility of Results ; }, abstract = {The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.}, }
@article {pmid39181078, year = {2024}, author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y}, title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.}, journal = {Ecotoxicology and environmental safety}, volume = {284}, number = {}, pages = {116916}, doi = {10.1016/j.ecoenv.2024.116916}, pmid = {39181078}, issn = {1090-2414}, mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; }, abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.}, }
@article {pmid39180071, year = {2024}, author = {Zhuang, M and Qiao, C and Han, L and Bi, Y and Cao, M and Wang, S and Guo, L and Pang, R and Xie, H}, title = {Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.}, journal = {Journal of nanobiotechnology}, volume = {22}, number = {1}, pages = {507}, pmid = {39180071}, issn = {1477-3155}, support = {2023YFD1400902//National Key Research and Development Program of China/ ; J210019//Beijing Municipal Natural Science Foundation/ ; C2021204190//Natural Science Foundation of Hebei Province/ ; 21JCZXJC00110//Natural Science Foundation of Tianjin Municipality/ ; }, mesh = {*Triticum ; *Rhizosphere ; *Bacteria/genetics/metabolism/drug effects ; *Microplastics ; *Soil Microbiology ; Nanoparticles/chemistry ; Stress, Physiological ; Microbiota ; Soil Pollutants ; Particle Size ; Polystyrenes/chemistry ; Multiomics ; }, abstract = {The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.}, }
@article {pmid39178805, year = {2024}, author = {Bravo-Ortiz, MA and Guevara-Navarro, E and Holguín-García, SA and Rivera-Garcia, M and Cardona-Morales, O and Ruz, GA and Tabares-Soto, R}, title = {SpectroCVT-Net: A convolutional vision transformer architecture and channel attention for classifying Alzheimer's disease using spectrograms.}, journal = {Computers in biology and medicine}, volume = {181}, number = {}, pages = {109022}, doi = {10.1016/j.compbiomed.2024.109022}, pmid = {39178805}, issn = {1879-0534}, mesh = {*Alzheimer Disease/classification/physiopathology/diagnosis ; Humans ; *Electroencephalography/methods ; *Signal Processing, Computer-Assisted ; Male ; Female ; Databases, Factual ; Aged ; }, abstract = {Dementia arises from various brain-affecting diseases and injuries, with Alzheimer's disease being the most prevalent, impacting around 55 million people globally. Current clinical diagnosis often relies on biomarkers indicative of Alzheimer's distinctive features. Electroencephalography (EEG) serves as a cost-effective, user-friendly, and safe biomarker for early Alzheimer's detection. This study utilizes EEG signals processed with Short-Time Fourier Transform (STFT) to generate spectrograms, facilitating visualization of EEG signal properties. Leveraging the Brainlat database, we propose SpectroCVT-Net, a novel convolutional vision transformer architecture incorporating channel attention mechanisms. SpectroCVT-Net integrates convolutional and attention mechanisms to capture local and global dependencies within spectrograms. Comprising feature extraction and classification stages, the model enhances Alzheimer's disease classification accuracy compared to transfer learning methods, achieving 92.59 ± 2.3% accuracy across Alzheimer's, healthy controls, and behavioral variant frontotemporal dementia (bvFTD). This article introduces a new architecture and evaluates its efficacy with unconventional data for Alzheimer's diagnosis, contributing: SpectroCVT-Net, tailored for EEG spectrogram classification without reliance on transfer learning; a convolutional vision transformer (CVT) module in the classification stage, integrating local feature extraction with attention heads for global context analysis; Grad-CAM analysis for network decision insight, identifying critical layers, frequencies, and electrodes influencing classification; and enhanced interpretability through spectrograms, illuminating key brain wave contributions to Alzheimer's, frontotemporal dementia, and healthy control classifications, potentially aiding clinical diagnosis and management.}, }
@article {pmid39178313, year = {2024}, author = {Du, J and Liu, W and Li, M and Li, Z and Li, X and Dai, Y and Liu, G and Wang, X and Zhu, P and Gladyshev, VN and Zhou, X}, title = {Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002778}, pmid = {39178313}, issn = {1545-7885}, mesh = {Animals ; Mice ; *Histones/metabolism ; Humans ; Neoplasms/genetics/metabolism/pathology ; Mole Rats/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Proteomics/methods ; Fibroblasts/metabolism ; Autophagy/genetics ; Adaptation, Physiological/genetics ; Transcriptome/genetics ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Signal Transduction ; Multiomics ; }, abstract = {The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.}, }
@article {pmid39176874, year = {2024}, author = {Knak, AK and Roheger, M and Wulff, A}, title = {Challenges in Daily Computerized Assessment of Cognitive Functions of Post-COVID Patients.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1950-1954}, doi = {10.3233/SHTI240815}, pmid = {39176874}, issn = {1879-8365}, mesh = {Humans ; *COVID-19 ; Cognitive Dysfunction ; Diagnosis, Computer-Assisted/methods ; SARS-CoV-2 ; Fatigue ; Post-Acute COVID-19 Syndrome ; Cognition ; }, abstract = {While it would be quite helpful to learn more about the daily fluctuations of fatigue and cognitive impairments of post-COVID patients, their condition can make investigating these especially challenging. By discussing these issues with post-COVID patients and clinical practitioners, we identified six challenges that specifically apply to daily computerized assessment of cognitive functions of post-COVID patients. We proposed solutions for each of the challenges which can be summarized as offering a carefully planned and flexible study design to participants and monitoring their well-being throughout the assessments. We argue that when the proposed precautions are taken, it is feasible to conduct a study that will generate valuable insights into the trajectories of (cognitive) post-COVID symptoms.}, }
@article {pmid39176504, year = {2024}, author = {Kokolakis, S and Kokinou, E and Chronaki, C and Moen, A and Datta, G}, title = {Earth Observation and Geoinformatics to Monitoring the Environmental Status of Urban Streams Inextricably Linked to People's Mental Health.}, journal = {Studies in health technology and informatics}, volume = {316}, number = {}, pages = {1560-1564}, doi = {10.3233/SHTI240716}, pmid = {39176504}, issn = {1879-8365}, mesh = {*Environmental Monitoring/methods ; Humans ; *Mental Health ; Rivers ; Geographic Information Systems ; Cities ; }, abstract = {The general condition of urban watercourses is inextricably linked to ecological balance and public health (physical and mental well-being). Given the vulnerability of these systems to climate change and human pollution, this work aims to demonstrate the effective use of environmental indicators to: a) rapidly assess soil and water conditions near urban streams and b) highlight the importance of geoinformatics and earth observation supported by ground-based techniques. There is a great need for new technology and methods for spatial and temporal monitoring and further quantification of environmental quality in urban streams and the land surrounding them to sensitize policymakers and the public to the environmental degradation of these exceptional habitats and to further protect people's mental health.}, }
@article {pmid39173171, year = {2024}, author = {Barahona, M and Alegría, A and Amstein, C and Cárcamo, M and Barahona, M}, title = {Epidemiology of high-energy trauma in Chile: An ecological analysis using public registries.}, journal = {Medwave}, volume = {24}, number = {7}, pages = {e2929}, doi = {10.5867/medwave.2024.07.2929}, pmid = {39173171}, issn = {0717-6384}, mesh = {Chile/epidemiology ; Humans ; *Accidents, Traffic/statistics & numerical data/mortality ; Male ; Adult ; *Databases, Factual ; *Registries ; Female ; Young Adult ; Middle Aged ; *Multiple Trauma/epidemiology/mortality ; Wounds and Injuries/epidemiology/mortality ; Public Health ; Sex Distribution ; Adolescent ; Age Distribution ; World Health Organization ; Aged ; }, abstract = {High-energy trauma is defined as severe organic injuries resulting from events that generate a large amount of kinetic, electrical, or thermal energy. It represents a significant public health concern, accounting for 10% of global mortality. This article aims to describe the epidemiology of high-energy trauma in Chile. Specifically, it seeks to compare the mortality rate per 100 000 inhabitants among member countries of the World Health Organization (WHO), provide a descriptive analysis of notifications under the Explicit Health Guarantees (GES) for the health issue of polytraumatized patients, and analyze the trend in the mortality rate due to external causes in Chile. This study employs an ecological design using three open-access databases. First, the WHO database on deaths from traffic accidents in 2019 was used. Then, the GES database was consulted for the "Polytraumatized" issue between 2018 and 2022. Finally, the Chilean Department of Health Statistics database on causes of death between 1997 and 2020 was utilized. In 2019, Chile ranked in the middle regarding the mortality rate per 100 000 inhabitants due to traffic accidents. GES notifications for polytrauma predominantly involved men aged 20 to 40 years and those affiliated with the public health system, highlighting a primary focus for prevention efforts. Mortality from accidents showed a decreasing trend, with significant structural changes identified in 2000 and 2007.}, }
@article {pmid39170344, year = {2024}, author = {D, S and Vellaturi, G and Shaik Ibrahim, SH and Molugu, S and Desanamukula, VS and Kocherla, R and Vatambeti, R}, title = {Enhanced deep learning models for automatic fish species identification in underwater imagery.}, journal = {Heliyon}, volume = {10}, number = {15}, pages = {e35217}, pmid = {39170344}, issn = {2405-8440}, abstract = {Underwater cameras are crucial in marine ecology, but their data management needs automatic species identification. This study proposes a two-stage deep learning approach. First, the Unsharp Mask Filter (UMF) preprocesses images. Then, an enhanced region-based fully convolutional network (R-FCN) detects fish using two-order integrals for position-sensitive score maps and precise region of interest (PS-Pr-RoI) pooling for accuracy. The second stage integrates ShuffleNetV2 with the Squeeze and Excitation (SE) module, forming the Improved ShuffleNetV2 model, enhancing classification focus. Hyperparameters are optimized with the Enhanced Northern Goshawk Optimization Algorithm (ENGO). The improved R-FCN model achieves 99.94 % accuracy, 99.58 % precision and recall, and a 99.27 % F-measure on the Fish4knowledge dataset. Similarly, the ENGO-based ShuffleNetV2 model, evaluated on the same dataset, shows 99.93 % accuracy, 99.19 % precision, 98.29 % recall, and a 98.71 % F-measure, highlighting its superior classification accuracy.}, }
@article {pmid39169276, year = {2024}, author = {Arcioni, L and Arcieri, M and Martino, JD and Liberati, F and Bottoni, P and Castrignanò, T}, title = {HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {272}, pmid = {39169276}, issn = {1471-2105}, support = {B87G22000450001//Ministry of University and Research, Italy/ ; }, mesh = {*Software ; *Transcriptome/genetics ; *Molecular Sequence Annotation/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Databases, Genetic ; }, abstract = {BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure.
RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software.
CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.}, }
@article {pmid39167718, year = {2024}, author = {Zass, L and Mwapagha, LM and Louis-Jacques, AF and Allali, I and Mulindwa, J and Kiran, A and Hanachi, M and Souiai, O and Mulder, N and Oduaran, OH}, title = {Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39167718}, issn = {1758-0463}, support = {U24 HG009780/HG/NHGRI NIH HHS/United States ; 1U24HG009780/NH/NIH HHS/United States ; }, mesh = {*Metadata ; *Microbiota ; Humans ; Databases, Factual ; }, abstract = {Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.}, }
@article {pmid39162518, year = {2024}, author = {Hu, D and Zhang, T and He, S and Pu, T and Yin, Y and Hu, Y}, title = {Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.}, journal = {Microbiology spectrum}, volume = {12}, number = {10}, pages = {e0086424}, pmid = {39162518}, issn = {2165-0497}, support = {32370552//MOST | National Natural Science Foundation of China (NSFC)/ ; 32070414,32325010//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Mammals/microbiology ; *Metagenome ; *Multigene Family ; Bacteria/genetics/classification/metabolism ; Polyketides/metabolism ; Data Mining ; Biological Products/metabolism ; Female ; Biosynthetic Pathways/genetics ; }, abstract = {Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.}, }
@article {pmid39161242, year = {2024}, author = {Setyawati, I and Husaini, AF and Setiawan, AG and Artika, IM and Ambarsari, L and Nurcholis, W and Vidilaseris, K and Kurniatin, PA}, title = {Structural Classification Insights Into the Plant Defensive Peptides.}, journal = {Proteins}, volume = {92}, number = {12}, pages = {1413-1427}, doi = {10.1002/prot.26736}, pmid = {39161242}, issn = {1097-0134}, support = {102/E5/PG.02.00.PL/2023//Ministry of Education, Culture, Research, and Technology, Republic of Indonesia/ ; }, mesh = {*Phylogeny ; *Plant Proteins/chemistry/genetics/metabolism ; *Plants/metabolism/chemistry ; *Databases, Protein ; Evolution, Molecular ; Amino Acid Sequence ; Models, Molecular ; }, abstract = {This study presents a structural phylogenetic analysis of plant defensive peptides, revealing their evolutionary relationships, structural diversification, and functional adaptations. Utilizing a robust dataset comprising both experimental and predicted structures sourced from the RCSB Protein Data Bank and AlphaFold DB, we constructed a detailed phylogenetic tree to elucidate the distinct evolutionary paths of plant defensive peptide families. Our findings showcase the evolutionary intricacies of defensive peptides, highlighting their diversity and the conservation of key structural motifs critical to their antimicrobial or defensive functions. The results also underscore the adaptive significance of defensive peptides in plant evolution, highlighting their roles in responding to ecological pressures and pathogen interactions.}, }
@article {pmid39155119, year = {2024}, author = {Reitz, ZL}, title = {Predicting metallophore structure and function through genome mining.}, journal = {Methods in enzymology}, volume = {702}, number = {}, pages = {371-401}, doi = {10.1016/bs.mie.2024.06.007}, pmid = {39155119}, issn = {1557-7988}, mesh = {*Genomics/methods ; Genome, Bacterial ; Computational Biology/methods ; Siderophores/metabolism/chemistry/genetics ; Data Mining/methods ; }, abstract = {Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.}, }
@article {pmid39154763, year = {2024}, author = {Lin, X and Sun, B and Wang, P and Zhao, M and Liu, D and Zhang, Q and Wu, B and Liu, D}, title = {Enhanced low-concentration phosphate adsorption using magnetic UiO-66@Fe3O4 composite with potential linker exchange.}, journal = {Chemosphere}, volume = {364}, number = {}, pages = {143126}, doi = {10.1016/j.chemosphere.2024.143126}, pmid = {39154763}, issn = {1879-1298}, mesh = {Adsorption ; *Phosphates/chemistry ; *Water Pollutants, Chemical/chemistry ; Water Purification/methods ; Metal-Organic Frameworks/chemistry ; Ferric Compounds/chemistry ; Magnetics ; Phthalic Acids ; }, abstract = {A magnetic FenUiO-66 adsorbent was created to achieve high phosphate adsorption capacity. The incorporation of Fe3O4 facilitated the precipitation and growth of UiO-66 during crystallization, resulting in a shift towards a multilayer heterogeneous distribution of adsorption sites. The increased Fe3O4 content notably enhanced the magnetic properties of FenUiO-66, while negligibly affecting its adsorption performance. The Fe1.5UiO-66 demonstrated exceptional phosphate adsorption capacity (136.54 mg/g), outstanding selectivity, and sustained reusability, with an 80% removal efficiency after nine cycles of treating actual water. The mechanism of phosphate adsorption by FenUiO-66 involved electrostatic attraction, ligand exchange, and linker exchange. Notably, while linker exchange significantly contributed to high adsorption capacity, it resulted in irreversible damage to the FenUiO-66 crystal. These unequivocal findings will serve as a solid foundation for further research and underline the critical role of linkers in the process of phosphate adsorption.}, }
@article {pmid39154477, year = {2024}, author = {Bai, Z and He, Y and Hu, G and Cheng, L and Wang, M}, title = {Microplastics at an environmentally relevant dose enhance mercury toxicity in a marine copepod under multigenerational exposure: Multi-omics perspective.}, journal = {Journal of hazardous materials}, volume = {478}, number = {}, pages = {135529}, doi = {10.1016/j.jhazmat.2024.135529}, pmid = {39154477}, issn = {1873-3336}, mesh = {Animals ; *Copepoda/drug effects ; *Mercury/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Reproduction/drug effects ; Apoptosis/drug effects ; Proteomics ; Multiomics ; }, abstract = {Here, we subjected the marine copepod Tigriopus japonicus to environmentally-relevant concentrations of microplastics (MPs) and mercury (Hg) for three generations (F0-F2) to investigate their physiological and molecular responses. Hg accumulation and phenotypic traits were measured in each generation, with multi-omics analysis conducted in F2. The results showed that MPs insignificantly impacted the copepod's development and reproduction, however, which were significantly compromised by Hg exposure. Interestingly, MPs significantly increased Hg accumulation and consequently aggravated this metal toxicity in T. japonicus, demonstrating their carrier role. Multi-omics analysis indicated that Hg pollution produced numerous toxic events, e.g., induction of apoptosis, damage to cell/organ morphogenesis, and disordered energy metabolism, ultimately resulting in retarded development and decreased fecundity. Importantly, MPs enhanced Hg toxicity mainly via increased oxidative apoptosis, compromised cell/organ morphogenesis, and energy depletion. Additionally, phosphoproteomic analysis revealed extensive regulation of the above processes, and also impaired neuron activity under combined MPs and Hg exposure. These alterations adversely affected development and reproduction of T. japonicus. Overall, our findings should offer novel molecular insights into the response of T. japonicus to long-term exposure to MPs and Hg, with a particular emphasis on the carrier role of MPs on Hg toxicity.}, }
@article {pmid39151562, year = {2024}, author = {Rahimian, M and Panahi, B}, title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.}, journal = {Virus research}, volume = {349}, number = {}, pages = {199450}, pmid = {39151562}, issn = {1872-7492}, mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; }, abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.}, }
@article {pmid39147186, year = {2024}, author = {Song, J and Zhou, S and Zou, D and Kwan, MP and Cai, J and Lu, J}, title = {Non-linear associations between noise level and people's short-term noise annoyance in different activity contexts.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119772}, doi = {10.1016/j.envres.2024.119772}, pmid = {39147186}, issn = {1096-0953}, mesh = {Humans ; Male ; Female ; Adult ; *Noise/adverse effects ; Young Adult ; Ecological Momentary Assessment ; Environmental Exposure ; Middle Aged ; Noise, Transportation/adverse effects ; Geographic Information Systems ; Nonlinear Dynamics ; }, abstract = {Recent research has become increasingly interested in the on-linear associations between noise levels and people's short-term noise annoyance. However, there has been limited investigation into measuring short-term noise annoyance and how different activity contexts may affect these non-linear associations. To address this research gap, this study measured people's short-term noise annoyance using real-time Ecological Momentary Assessment (EMA) data and the Day Reconstruction Method's (DRM) recalled data. Corresponding noise levels were captured using Global Positioning Systems and portable noise sensors. Employing the Shapley additive explanations method, we examined the non-linear associations between noise level and people's real-time and recalled noise annoyance across different activity contexts. The results indicated that 1) People had greater sensitivity to noise levels in real-time annoyance (non-linear association threshold: 60 dB) compared to recalled annoyance, which had a higher non-linear association threshold of 70 dB. 2) The non-linear associations between noise level and people's real-time/recalled noise annoyance varied between different activity contexts. People tended to be more sensitive to noise in real-time annoyance than recalled annoyance on travel routes and at workplaces. 3) Among the factors examined, the contribution of noise level varied across activity contexts. Noise level contributed more significantly to people's real-time noise annoyance in outdoor recreational sites and on travel routes. These findings enhance our understanding of the non-linear association between noise level and people's short-term noise annoyance, moving beyond the linear paradigm. Policymakers should consider the non-linear relationships and different activity contexts when implementing noise control measures.}, }
@article {pmid39146704, year = {2024}, author = {Li, G and Wu, M and Xiao, Y and Tong, Y and Li, S and Qian, H and Zhao, T}, title = {Multi-omics reveals the ecological and biological functions of Enterococcus mundtii in the intestine of lepidopteran insects.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {52}, number = {}, pages = {101309}, doi = {10.1016/j.cbd.2024.101309}, pmid = {39146704}, issn = {1878-0407}, mesh = {Animals ; *Bombyx/microbiology/genetics ; *Enterococcus/genetics ; *Gastrointestinal Microbiome ; *Intestines/microbiology ; Proteomics ; Symbiosis ; Multiomics ; }, abstract = {Insect guts offer unique habitats for microbial colonization, with gut bacteria potentially offering numerous benefits to their hosts. Although Enterococcus has emerged as one of the predominant gut commensal bacteria in insects, its establishment in various niches within the gut has not been characterized well. In this study, Enterococcus mundtii was inoculated into the silkworm (Bombyx mori L.) to investigate its biological functions. Genome-based analysis revealed that its successful colonization is related to adherence genes (ebpA, ebpC, efaA, srtC, and scm). This bacterium did not alter the activities of related metabolic enzymes or the intestinal barrier function. However, significant changes in the gene expressions levels of Att2, CecA, and Lys suggest potential adaptive mechanisms of host immunity to symbiotic E. mundtii. Moreover, 16S metagenomics analysis revealed a significant increase in the relative abundance of E. mundtii in the intestines of silkworms following inoculation. The intestinal microbiome displayed marked heterogeneity, an elevated gut microbiome health index, a reduced microbial dysbiosis index, and low potential pathogenicity in the treatment group. Additionally, E. mundtii enhanced the breakdown of carbohydrates in host intestines. Overall, E. mundtii serves as a beneficial microbe for insects, promoting intestinal homeostasis by providing competitive advantage. This characteristic helps E. mundtii dominate complex microbial environments and remain prevalent across Lepidoptera, likely fostering long-term symbiosis between the both parties. The present study contributes to clarifying the niche of E. mundtii in the intestine of lepidopteran insects and further reveals its potential roles in their insect hosts.}, }
@article {pmid39146377, year = {2024}, author = {Nuismer, SL and Basinski, AJ and Schreiner, CL and Eskew, EA and Fichet-Calvet, E and Remien, CH}, title = {Quantifying the risk of spillover reduction programs for human health.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012358}, pmid = {39146377}, issn = {1553-7358}, support = {R01 GM122079/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Computer Simulation ; *Zoonoses/transmission/epidemiology/prevention & control/virology ; Computational Biology ; Public Health ; Lassa Fever/epidemiology/prevention & control/transmission ; Disease Outbreaks/prevention & control/statistics & numerical data ; Risk Assessment ; Africa, Western/epidemiology ; }, abstract = {Reducing spillover of zoonotic pathogens is an appealing approach to preventing human disease and minimizing the risk of future epidemics and pandemics. Although the immediate human health benefit of reducing spillover is clear, over time, spillover reduction could lead to counterintuitive negative consequences for human health. Here, we use mathematical models and computer simulations to explore the conditions under which unanticipated consequences of spillover reduction can occur in systems where the severity of disease increases with age at infection. Our results demonstrate that, because the average age at infection increases as spillover is reduced, programs that reduce spillover can actually increase population-level disease burden if the clinical severity of infection increases sufficiently rapidly with age. If, however, immunity wanes over time and reinfection is possible, our results reveal that negative health impacts of spillover reduction become substantially less likely. When our model is parameterized using published data on Lassa virus in West Africa, it predicts that negative health outcomes are possible, but likely to be restricted to a small subset of populations where spillover is unusually intense. Together, our results suggest that adverse consequences of spillover reduction programs are unlikely but that the public health gains observed immediately after spillover reduction may fade over time as the age structure of immunity gradually re-equilibrates to a reduced force of infection.}, }
@article {pmid39146316, year = {2024}, author = {He, YJ and Liao, H and Yang, G and Qiu, W and Xuan, R and Zheng, G and Xu, B and Yang, X and Magnuson, JT and Schlenk, D and Zheng, C}, title = {Perfluorohexanesulfonic Acid (PFHxS) Impairs Lipid Homeostasis in Zebrafish Larvae through Activation of PPARα.}, journal = {Environmental science & technology}, volume = {58}, number = {37}, pages = {16258-16268}, doi = {10.1021/acs.est.4c03053}, pmid = {39146316}, issn = {1520-5851}, mesh = {Animals ; *Zebrafish ; *Larva/drug effects/metabolism ; *Homeostasis ; *PPAR alpha/metabolism ; Lipid Metabolism/drug effects ; Fluorocarbons ; Sulfonic Acids ; }, abstract = {Perfluorohexanesulfonic acid (PFHxS), an emerging short-chain per- and polyfluoroalkyl substance, has been frequently detected in aquatic environments. Adverse outcome pathway studies have shown that perfluorinated compounds impair lipid homeostasis through peroxisome proliferator activated receptors (PPARs). However, many of these studies were performed at high concentrations and may thus be a result of overt toxicity. To better characterize the molecular and key events of PFHxS to biota, early life-stage zebrafish (Danio rerio) were exposed to concentrations detected in the environment (0.01, 0.1, 1, and 10 μg/L). Lipidomic and transcriptomic evaluations were integrated to predict potential molecular targets. PFHxS significantly impaired lipid homeostasis by the dysregulation of glycerophospholipids, fatty acyls, glycerolipids, sphingolipids, prenol lipids, and sterol lipids. Informatic analyses of the lipidome and transcriptome indicated alterations of the PPAR signaling pathway, with downstream changes to retinol, linoleic acid, and glycerophospholipid metabolism. To assess the role of PPARs, potential binding of PFHxS to PPARs was predicted and animals were coexposed to a PPAR antagonist (GW6471). Molecular simulation indicated PFHxS had a 27.1% better binding affinity than oleic acid, an endogenous agonist of PPARα. Antagonist coexposures rescued impaired glycerophosphocholine concentrations altered by PFHxS. These data indicate PPARα activation may be an important molecular initiating event for PFHxS.}, }
@article {pmid39145536, year = {2024}, author = {Pipes, L and Nielsen, R}, title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39145536}, issn = {2050-084X}, support = {BIO180028//Pittsburgh Supercomputing Center/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support/ ; R01 GM138634/GM/NIGMS NIH HHS/United States ; K99 GM144747/GM/NIGMS NIH HHS/United States ; }, mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.}, }
@article {pmid39145283, year = {2023}, author = {Boyes, D and Skojec, C and Kawahara, AY and , and , and , and , and , and , }, title = {The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {342}, pmid = {39145283}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.}, }
@article {pmid39143756, year = {2024}, author = {Bauer, IE and Davies, MA and Bona, KA and Hararuk, O and Shaw, CH and Thompson, DK and Kurz, WA and Webster, KL and Garneau, M and McLaughlin, JW and Packalen, MS and Prystupa, E and Sanderson, NK and Tarnocai, C}, title = {Peat profile database from peatlands in Canada.}, journal = {Ecology}, volume = {105}, number = {10}, pages = {e4398}, doi = {10.1002/ecy.4398}, pmid = {39143756}, issn = {1939-9170}, support = {//Government of Canada (Expanding Market Opportunities Program)/ ; }, mesh = {Canada ; *Soil/chemistry ; Databases, Factual ; Ecosystem ; }, abstract = {Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial- to millennial-scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was developed by the Canadian Forest Service. Model parameterization included compiling peat profiles across Canada to calibrate peat decomposition rates from different peatland types, to define typical bulk density profiles, and to describe the hydrological (i.e., water table) response of peatlands to climatic changes. A total of 1217 sites were included in the dataset from published and unpublished sources. The CORESITES table contains site location and summary data for each profile, as well as an estimate of total carbon mass per unit area (in megagrams of C per hectare). Total carbon mass per unit area at each location was calculated using bulk density and carbon content through each profile. The PROFILES table contains data for depth (in centimeters), bulk density (in grams per cubic meter), ash and carbon content (in percentage), and material descriptions for contiguous samples through each peat profile. Data gaps for bulk density and C content were filled using interpolation, regression trees, and assigned values based on material description and/or soil classification to allow for the estimation of total carbon mass per unit area. A subset of the sites (N = 374) also have pH and pore water trace-elemental geochemistry data and are found in the WATER table. The REFERENCES table contains the full citation of each source of the data and is linked to each core location through the SOURCEDATA table. The LOOKUP table defines codes in the database that required more space that what was sufficient in the metadata tables. The data can be accessed on Open Government Canada and will be useful for future work on carbon stock mapping and ecosystem modeling. All metadata and data are provided © Her Majesty the Queen in Right of Canada, 2023 and information contained in this publication may be reproduced for personal or public noncommercial purposes with attribution, whereas commercial reproduction and distribution are prohibited except with written permission from NRCan; complete details are noted in the Supporting Information file Metadata S1 (see Class III.B.3: Copyright restrictions).}, }
@article {pmid39140146, year = {2024}, author = {Yang, F and Han, QL and Zhao, WD and Zhao, Y}, title = {EC number prediction of protein sequences based on combination of hierarchical and global features.}, journal = {Yi chuan = Hereditas}, volume = {46}, number = {8}, pages = {661-669}, doi = {10.16288/j.yczz.24-102}, pmid = {39140146}, issn = {0253-9772}, mesh = {*Computational Biology/methods ; Amino Acid Sequence ; Proteins/chemistry ; Algorithms ; Sequence Analysis, Protein/methods ; Enzymes/chemistry/metabolism ; }, abstract = {The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.}, }
@article {pmid39139763, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen & Karsholt, 2017).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {357}, pmid = {39139763}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Anarsia innoxiella (the Acer Sober; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 302.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.}, }
@article {pmid39139615, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {143}, pmid = {39139615}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.}, }
@article {pmid39139614, year = {2024}, author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {211}, pmid = {39139614}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.}, }
@article {pmid39137474, year = {2024}, author = {Tanaka, S and Uraguchi, K and Suzuki, E and Matsumoto, N and Tsumura, M and Fujimoto, S and Miyamoto, S and Yorifuji, T and Ando, M}, title = {Survey of pharyngeal foreign bodies in Japan: An ecological study using the nationwide claims data.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {184}, number = {}, pages = {112055}, doi = {10.1016/j.ijporl.2024.112055}, pmid = {39137474}, issn = {1872-8464}, mesh = {Humans ; *Foreign Bodies/epidemiology ; Japan/epidemiology ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; Infant ; Adult ; *Pharynx ; Young Adult ; Feeding Behavior ; Middle Aged ; Incidence ; Databases, Factual ; Seasons ; Aged ; Sex Distribution ; Age Distribution ; }, abstract = {OBJECTIVE: Pharyngeal foreign bodies (PFBs) are a prevalent disease affected by food culture and dietary habits, with fish bones as the leading cause. Most studies were limited to specific regions, and a nationwide survey was not conducted in Japan. In this ecological study, we aimed to conduct a nationwide analysis of outpatient PFB cases in Japan over three years, focusing on seasonal trends, sex- and age-stratified cases, and regional differences.
METHODS: We used the National Database of Health Insurance Claims and Specific Health Checkups of Japan open data from April 2019 to March 2022. The case data were analyzed by month, age, sex, and prefecture. Additionally, we calculated the standardized claim ratios (SCRs) for each prefecture and investigated the association between dietary habits, food culture, and SCR of PFBs using a two-level linear regression model.
RESULTS: We analyzed a total of 164,337 outpatient PFB cases in Japan, revealing an average incidence rate of 45.6 per 100,000 persons. The seasonal trend revealed a peak in July each year from 2019 to 2021, confirming seasonality in PFB incidents. Children reported a higher incidence rate. Living west of Japan and expenditure on fish and shellfish had a strongly positive association with the SCR of PFBs.
CONCLUSION: Our nationwide survey reveals that, even within Japan, there were regional variations influenced by food culture and dietary habits. The data showed that PFB incidence was higher among children, highlighting the need for preventive education.
LEVEL OF EVIDENCE: Level 3.}, }
@article {pmid39133313, year = {2024}, author = {Kuchař, M and Kotěrová, AP and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Correction to: Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2739}, doi = {10.1007/s00414-024-03311-2}, pmid = {39133313}, issn = {1437-1596}, }
@article {pmid39132840, year = {2024}, author = {Vale, FF and Roberts, RJ and Kobayashi, I and Camargo, MC and Rabkin, CS and , }, title = {Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2379440}, pmid = {39132840}, issn = {1949-0984}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R03 CA167773/CA/NCI NIH HHS/United States ; K22 CA226395/CA/NCI NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; R01 DK062813/DK/NIDDK NIH HHS/United States ; K07 CA125588/CA/NCI NIH HHS/United States ; P01 CA028842/CA/NCI NIH HHS/United States ; K08 CA252635/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; R01 CA190612/CA/NCI NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; R01 ES010178/ES/NIEHS NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {*Helicobacter pylori/genetics/virology ; *Prophages/genetics/physiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; *Genomics ; Helicobacter Infections/microbiology ; }, abstract = {Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.}, }
@article {pmid39131439, year = {2024}, author = {Menger, J and Magagna, B and Henle, K and Harpke, A and Frenzel, M and Rick, J and Wiltshire, K and Grimm-Seyfarth, A}, title = {FAIR-EuMon: a FAIR-enabling resource for biodiversity monitoring schemes.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e125132}, pmid = {39131439}, issn = {1314-2828}, abstract = {BACKGROUND: Within the scope of the Helmholtz Metadata Collaboration (HMC), the ADVANCE project - Advanced metadata standards for biodiversity survey and monitoring data: supporting of research and conservation - aimed at supporting rich metadata generation with interoperable metadata standards and semantic artefacts that facilitate data access, integration and reuse across terrestrial, freshwater and marine realms. HMC's mission is to facilitate the discovery, access, machine-readability, and reuse of research data across and beyond the Helmholtz Association.
NEW INFORMATION: We revised, adapted and expanded existing metadata schemas, vocabularies and thesauri to build a FAIR metadata schema and a metadata entry form built on it for users to provide their metadata instances focused on biodiversity monitoring data. The schema is FAIR because it is both machine-interpretable and follows domain-relevant community standards. This report provides a general overview of the project results and instructions on how to access, re-use and complete the metadata form.}, }
@article {pmid39131363, year = {2024}, author = {Martin, C and Gitter, A and Anantharaman, K}, title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131363}, issn = {2692-8205}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.}, }
@article {pmid39131277, year = {2024}, author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Anez, GM and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Roha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE}, title = {Complete sequencing of ape genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39131277}, issn = {2692-8205}, support = {R01 MH120295/MH/NIMH NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P51 OD011092/OD/NIH HHS/United States ; R56 AG056169/AG/NIA NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; }, abstract = {We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.}, }
@article {pmid39129912, year = {2023}, author = {Boyes, D and Hutchinson, F and , and , and , and , and , and , }, title = {The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {547}, pmid = {39129912}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Charanyca ferruginea (the Brown Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 854.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,126 protein coding genes.}, }
@article {pmid39127755, year = {2024}, author = {Pekár, S}, title = {Datasets of traits of zodariid spiders (Araneae: Zodariidae).}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {862}, pmid = {39127755}, issn = {2052-4463}, mesh = {*Spiders/classification/anatomy & histology/physiology ; Animals ; Ecosystem ; Databases, Factual ; Australia ; }, abstract = {Species traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.}, }
@article {pmid39122728, year = {2024}, author = {Hixon, SW and Fernandes, R and Andriamahaihavana, A and Baden, AL and Blanco, MB and Caulier, G and Dammhahn, M and Eeckhaut, I and Eppley, TM and Frédérich, B and Ganzhorn, JU and Garbaras, A and Gibson, D and Goodman, SM and Irwin, M and Kelley, EA and Michel, LN and Lepoint, G and Loudon, JE and Mittelheiser, L and Rakotondranary, J and Rasamisoa, DC and Rasolofonirina, R and Ratovonamana, Y and Razafindramanana, J and Reisdorff, C and Sponheimer, M and Terrana, L and Vasey, N and Crowley, BE}, title = {Introducing IsoMad, a compilation of isotopic datasets for Madagascar.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {857}, pmid = {39122728}, issn = {2052-4463}, mesh = {Madagascar ; *Databases, Factual ; Animals ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; }, abstract = {We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.}, }
@article {pmid39122322, year = {2024}, author = {Martín, G and Erinjery, JJ and Ediriweera, D and Goldstein, E and Somaweera, R and de Silva, HJ and Lalloo, DG and Iwamura, T and Murray, KA}, title = {Effects of global change on snakebite envenoming incidence up to 2050: a modelling assessment.}, journal = {The Lancet. Planetary health}, volume = {8}, number = {8}, pages = {e533-e544}, pmid = {39122322}, issn = {2542-5196}, mesh = {*Snake Bites/epidemiology ; Incidence ; Sri Lanka/epidemiology ; Humans ; *Climate Change ; Models, Theoretical ; Forecasting ; Animals ; Snakes ; }, abstract = {BACKGROUND: Human activities are driving climate, land cover, and population change (global change), and shifting the baseline geographical distribution of snakebite. The interacting effects of global change on snakes and communities at risk of snakebite are poorly understood, limiting capacity to anticipate and manage future changes in snakebite risk.
METHODS: In this modelling study, we projected how global change will affect snakebite envenoming incidence in Sri Lanka, as a model system that has a high incidence of snakebite. We used the shared socioeconomic pathway (SSP) scenario analysis framework to integrate forecasts across the domains of: climate change (historical trend from WorldClim plus three underlying regional circulation models [RCMs] in the Coordinated Regional Downscaling Experiment-South Asia repository, with two emissions pathways [representative concentration pathways RCP4.5 and RCP8.5]); land cover change (Dyna-CLUE model); and human population density change (based on Gridded Population of the World data) from Jan 1, 2010 to Dec 31, 2050. Forecasts were integrated under three different development scenarios: a sustainability pathway (SSP1 and no further emissions), a middle-of-the-road pathway (SSP2 and RCP4.5), and a fossil-fuelled pathway (SSP5 and RCP8.5). For SSP2 and SSP5, we nested three different RCMs (CNRM-CM5, GFDL-CCM3, and MPI-ESM-LR; mean averaged to represent consensus) to account for variability in climate predictions. Data were used as inputs to a mechanistic model that predicted snakebite envenoming incidence based on human-snake contact patterns.
FINDINGS: From 2010 to 2050, at the national level, envenoming incidence in Sri Lanka was projected to decrease by 12·0-23·0%, depending on the scenario. The rate of decrease in envenoming incidence was higher in SSP5-RCP8.5 than in SSP1 and SSP2-RCP4.5. Change in envenoming incidence was heterogenous across the country. In SSP1, incidence decreased in urban areas expected to have population growth, and with land cover changes towards anthropised classes. In SSP2-RCP4.5 and SSP5-RCP8.5, most areas were projected to have decreases in incidence (SSP5-RCP8.5 showing the largest area with incidence reductions), while areas such as the central highlands and the north of the country showed localised increases. In the model, decreases occurred with human population growth, land use change towards anthropised classes (potentially shifting occupational risk factors), and decreasing abundance of some snake species, potentially due to global warming and reduced climatic and habitat suitability, with displacement of some snake species.
INTERPRETATION: Snakebite envenoming incidence was projected to decrease overall in the coming decades in Sri Lanka, but with an apparent emerging conflict with sustainability objectives. Therefore, efforts to mitigate snakebite envenoming incidence will need to consider the potential impacts of sustainability interventions, particularly related to climate and land use change and in areas where increases in incidence are projected. In view of global change, neglected tropical diseases and public health issues related to biodiversity, such as snakebite, should be managed collaboratively by both environment and health stakeholders.
FUNDING: UK Medical Research Council.}, }
@article {pmid39116194, year = {2024}, author = {Guseva, K and Mohrlok, M and Alteio, L and Schmidt, H and Pollak, S and Kaiser, C}, title = {Bacteria face trade-offs in the decomposition of complex biopolymers.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012320}, pmid = {39116194}, issn = {1553-7358}, mesh = {Biopolymers/metabolism/chemistry ; *Bacteria/metabolism/enzymology ; Models, Biological ; Computational Biology ; }, abstract = {Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.}, }
@article {pmid39114815, year = {2023}, author = {Lohse, K and Ebdon, S and Mackintosh, A and Martin, S and Saccheri, IJ and Bourn, NAD and Vila, R and , and , and , and , }, title = {The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {369}, pmid = {39114815}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.}, }
@article {pmid39114490, year = {2024}, author = {Butlin, R and Mérot, C and , and , and , and , and , }, title = {The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {197}, pmid = {39114490}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.}, }
@article {pmid39112823, year = {2024}, author = {Darabi, H and Bazhdar, Y and Ehsani, AH}, title = {Modeling the spatial relationship between landscape services and vulnerability assessment.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {9}, pages = {797}, pmid = {39112823}, issn = {1573-2959}, mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; *Ecosystem ; Iran ; Remote Sensing Technology ; Models, Theoretical ; Spatial Analysis ; }, abstract = {Even though many studies have been thus far devoted to landscape services (LS) or vulnerability assessment (VA) alone, the relationship between these two concepts has been less investigated. The current study attempts to model the spatial relationship between LS and VA in the Tarhan area (west of Iran). For this purpose, a combination of the analytic hierarchy process (AHP), remote sensing (RS), and geographic information system (GIS) techniques are applied to assess vulnerability. Variogram models and geostatistical simulations are used for mapping and evaluating landscape services. Moreover, the geographically weighted regression (GWR) is operated to predict the relationship between LS and VA. The results indicate that landform and socioeconomic variables are also two main factors shaping variations in VA. As well, the levels of services provided in the possible landscape are affected by the vulnerability. The assessment accordingly establishes that natural and cultural values have significant effects on services, in terms of their spatial distribution and nature. Exploring the relationship between LS and VA correspondingly depicts that VA has a direct influence on the capacity and entity of LS provision (adjusted R[2] = 0.67). The outcomes of the study provide a foundation for nature management and conservation, although it is less able to analyze the trade-off between ecosystem degradation and future development trends. The nexus of LS and future ecological processes in an integrated system can be thus the subject of further research.}, }
@article {pmid39109333, year = {2024}, author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , }, title = {The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {135}, pmid = {39109333}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Nymphula nitidulata (the Beautiful China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 635.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,031 protein coding genes.}, }
@article {pmid39109332, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {242}, pmid = {39109332}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from a male Zelleria hepariella (the Brown Ash Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 428.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,718 protein coding genes.}, }
@article {pmid39108663, year = {2023}, author = {Taylor, SC and Crowley, LM and Luker, S and Harvey, M and , and , and , and , and , and , and , }, title = {The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {526}, pmid = {39108663}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Villa cingulata (the Downland Villa bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 412.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.43 kilobases in length.}, }
@article {pmid39103962, year = {2024}, author = {Prakofjewa, J and Sartori, M and Kalle, R and Łuczaj, Ł and Karbarz, M and Mattalia, G and Šarka, P and Prūse, B and Stryamets, N and Anegg, M and Kuznetsova, N and Kolosova, V and Belichenko, O and Aziz, MA and Pieroni, A and Sõukand, R}, title = {"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {22}, pmid = {39103962}, issn = {2210-6340}, support = {714874//HORIZON EUROPE European Research Council/ ; }, abstract = {Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.}, }
@article {pmid39103035, year = {2024}, author = {Shi, C and Cheng, L and Yu, Y and Chen, S and Dai, Y and Yang, J and Zhang, H and Chen, J and Geng, N}, title = {Multi-omics integration analysis: Tools and applications in environmental toxicology.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {360}, number = {}, pages = {124675}, doi = {10.1016/j.envpol.2024.124675}, pmid = {39103035}, issn = {1873-6424}, mesh = {*Environmental Pollutants/toxicity ; *Ecotoxicology/methods ; *Proteomics ; Genomics ; Metabolomics ; Animals ; Humans ; Multiomics ; }, abstract = {Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.}, }
@article {pmid39102402, year = {2024}, author = {Saad-Roy, CM and Morris, SE and Boots, M and Baker, RE and Lewis, BL and Farrar, J and Marathe, MV and Graham, AL and Levin, SA and Wagner, CE and Metcalf, CJE and Grenfell, BT}, title = {Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.}, journal = {PLoS computational biology}, volume = {20}, number = {8}, pages = {e1012211}, pmid = {39102402}, issn = {1553-7358}, support = {U01 CK000555/CK/NCEZID CDC HHS/United States ; }, mesh = {Humans ; *COVID-19/immunology/prevention & control/epidemiology ; *SARS-CoV-2/immunology ; *COVID-19 Vaccines/immunology ; Vaccination Hesitancy/statistics & numerical data ; Severity of Illness Index ; Vaccination/statistics & numerical data ; Pandemics/prevention & control ; Computational Biology ; }, abstract = {The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.}, }
@article {pmid39102091, year = {2024}, author = {Kuchař, M and Pilmann Kotěrová, A and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J}, title = {Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.}, journal = {International journal of legal medicine}, volume = {138}, number = {6}, pages = {2647-2658}, pmid = {39102091}, issn = {1437-1596}, mesh = {Humans ; *Sex Determination by Skeleton/methods ; Male ; Female ; *Pelvic Bones/diagnostic imaging ; *Algorithms ; *Imaging, Three-Dimensional ; *Forensic Anthropology/methods ; Adult ; Middle Aged ; Aged ; Young Adult ; Portugal ; Aged, 80 and over ; }, abstract = {Thanks to technical progress and the availability of virtual data, sex estimation methods as part of a biological profile are undergoing an inevitable evolution. Further reductions in subjectivity, but potentially also in measurement errors, can be brought by approaches that automate the extraction of variables. Such automatization also significantly accelerates and facilitates the specialist's work. The aim of this study is (1) to apply a previously proposed algorithm (Kuchař et al. 2021) to automatically extract 10 variables used for the DSP2 sex estimation method, and (2) to test the robustness of the new automatic approach in a current heterogeneous population. For the first aim, we used a sample of 240 3D scans of pelvic bones from the same individuals, which were measured manually for the DSP database. For the second aim a sample of 108 pelvic bones from the New Mexico Decedent Image Database was used. The results showed high agreement between automatic and manual measurements with rTEM below 5% for all dimensions except two. The accuracy of final sex estimates based on all 10 variables was excellent (error rate 0.3%). However, we observed a higher number of undetermined individuals in the Portuguese sample (25% of males) and the New Mexican sample (36.5% of females). In conclusion, the procedure for automatic dimension extraction was successfully applied both to a different type of data and to a heterogeneous population.}, }
@article {pmid39101049, year = {2024}, author = {Boyes, D and Lees, DC and Holland, PWH and , and , and , and , and , and , and , and , }, title = {The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {35}, pmid = {39101049}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Biston strataria (the Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 424.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,406 protein coding genes.}, }
@article {pmid39100235, year = {2024}, author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A}, title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.}, journal = {Evolution letters}, volume = {8}, number = {4}, pages = {526-538}, pmid = {39100235}, issn = {2056-3744}, abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.}, }
@article {pmid39099847, year = {2024}, author = {Kapsetaki, SE and Compton, ZT and Dolan, J and Harris, VΚ and Mellon, W and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, AΜ and Maley, CC}, title = {Life history traits and cancer prevalence in birds.}, journal = {Evolution, medicine, and public health}, volume = {12}, number = {1}, pages = {105-116}, pmid = {39099847}, issn = {2050-6201}, support = {R01 CA140657/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND AND OBJECTIVES: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.
METHODOLOGY: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.
RESULTS: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.
CONCLUSIONS AND IMPLICATIONS: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.}, }
@article {pmid39099645, year = {2023}, author = {Obbard, DJ and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {477}, pmid = {39099645}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Chymomyza fuscimana (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 338.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.}, }
@article {pmid39092794, year = {2024}, author = {Ma, X and Huete, A and Liu, Y and Zhu, X and Nguyen, H and Miura, T and Chen, M and Li, X and Asrar, G}, title = {A holistic big data approach to understand and manage increasing pollen-induced respiratory allergies under global change.}, journal = {Global change biology}, volume = {30}, number = {8}, pages = {e17451}, doi = {10.1111/gcb.17451}, pmid = {39092794}, issn = {1365-2486}, support = {1027576//National Institute of Food and Agriculture/ ; DP210100347//Australian Research Council/ ; 42171305//National Natural Science Foundation of China/ ; }, mesh = {*Pollen/immunology ; *Big Data ; *Climate Change ; Humans ; Respiratory Hypersensitivity/etiology ; }, }
@article {pmid39092001, year = {2024}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , }, title = {The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {160}, pmid = {39092001}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Synanthedon andrenaeformis (the Orange-tailed Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 348.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.65 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,867 protein coding genes.}, }
@article {pmid39090383, year = {2024}, author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H}, title = {Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.}, journal = {Nature methods}, volume = {21}, number = {10}, pages = {1959}, doi = {10.1038/s41592-024-02395-3}, pmid = {39090383}, issn = {1548-7105}, }
@article {pmid39089617, year = {2024}, author = {Chen, SH and Chen, CH and Lin, HC and Yeh, SA and Hwang, TL and Chen, PJ}, title = {Drug repurposing of cyclin-dependent kinase inhibitors for neutrophilic acute respiratory distress syndrome and psoriasis.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.07.026}, pmid = {39089617}, issn = {2090-1224}, abstract = {BACKGROUND: Neutrophilic inflammation, characterized by dysregulated neutrophil activation, triggers a variety of inflammatory responses such as chemotactic infiltration, oxidative bursts, degranulation, neutrophil extracellular traps (NETs) formation, and delayed turnover. This type of inflammation is pivotal in the pathogenesis of acute respiratory distress syndrome (ARDS) and psoriasis. Despite current treatments, managing neutrophil-associated inflammatory symptoms remains a significant challenge.
AIM OF REVIEW: This review emphasizes the role of cyclin-dependent kinases (CDKs) in neutrophil activation and inflammation. It aims to highlight the therapeutic potential of repurposing CDK inhibitors to manage neutrophilic inflammation, particularly in ARDS and psoriasis. Additionally, it discusses the necessary precautions for the clinical application of these inhibitors due to potential off-target effects and the need for dose optimization.
CDKs regulate key neutrophilic functions, including chemotactic responses, degranulation, NET formation, and apoptosis. Repurposing CDK inhibitors, originally developed for cancer treatment, shows promise in controlling neutrophilic inflammation. Clinical anticancer drugs, palbociclib and ribociclib, have demonstrated efficacy in treating neutrophilic ARDS and psoriasis by targeting off-label pathways, phosphoinositide 3-kinase (PI3K) and phosphodiesterase 4 (PDE4), respectively. While CDK inhibitors offer promising therapeutic benefits, their clinical repurposing requires careful consideration of off-target effects and dose optimization. Further exploration and clinical trials are necessary to ensure their safety and efficacy in treating inflammatory conditions.}, }
@article {pmid39086664, year = {2023}, author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , }, title = {The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis & Schiffermüller, 1775).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {516}, pmid = {39086664}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.}, }
@article {pmid39083325, year = {2024}, author = {Webb, EK and Stevens, JS and Ely, TD and Lebois, LAM and van Rooij, SJH and Bruce, SE and House, SL and Beaudoin, FL and An, X and Neylan, TC and Clifford, GD and Linnstaedt, SD and Germine, LT and Bollen, KA and Rauch, SL and Haran, JP and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Murty, VP and Hudak, LA and Pascual, JL and Seamon, MJ and Datner, EM and Pearson, C and Peak, DA and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Joormann, J and Pizzagalli, DA and Harte, SE and Kessler, RC and Koenen, KC and Ressler, KJ and McLean, SA and Harnett, NG}, title = {Neighborhood Resources Associated With Psychological Trajectories and Neural Reactivity to Reward After Trauma.}, journal = {JAMA psychiatry}, volume = {81}, number = {11}, pages = {1090-1100}, pmid = {39083325}, issn = {2168-6238}, support = {K01 MH129828/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Stress Disorders, Post-Traumatic/physiopathology/diagnostic imaging ; Female ; Male ; *Reward ; Adult ; *Magnetic Resonance Imaging ; *Resilience, Psychological ; Longitudinal Studies ; *Residence Characteristics ; Middle Aged ; Young Adult ; Brain/physiopathology/diagnostic imaging ; Survivors/psychology ; }, abstract = {IMPORTANCE: Research on resilience after trauma has often focused on individual-level factors (eg, ability to cope with adversity) and overlooked influential neighborhood-level factors that may help mitigate the development of posttraumatic stress disorder (PTSD).
OBJECTIVE: To investigate whether an interaction between residential greenspace and self-reported individual resources was associated with a resilient PTSD trajectory (ie, low/no symptoms) and to test if the association between greenspace and PTSD trajectory was mediated by neural reactivity to reward.
As part of a longitudinal cohort study, trauma survivors were recruited from emergency departments across the US. Two weeks after trauma, a subset of participants underwent functional magnetic resonance imaging during a monetary reward task. Study data were analyzed from January to November 2023.
EXPOSURES: Residential greenspace within a 100-m buffer of each participant's home address was derived from satellite imagery and quantified using the Normalized Difference Vegetation Index and perceived individual resources measured by the Connor-Davidson Resilience Scale (CD-RISC).
MAIN OUTCOME AND MEASURES: PTSD symptom severity measured at 2 weeks, 8 weeks, 3 months, and 6 months after trauma. Neural responses to monetary reward in reward-related regions (ie, amygdala, nucleus accumbens, orbitofrontal cortex) was a secondary outcome. Covariates included both geocoded (eg, area deprivation index) and self-reported characteristics (eg, childhood maltreatment, income).
RESULTS: In 2597 trauma survivors (mean [SD] age, 36.5 [13.4] years; 1637 female [63%]; 1304 non-Hispanic Black [50.2%], 289 Hispanic [11.1%], 901 non-Hispanic White [34.7%], 93 non-Hispanic other race [3.6%], and 10 missing/unreported [0.4%]), 6 PTSD trajectories (resilient, nonremitting high, nonremitting moderate, slow recovery, rapid recovery, delayed) were identified through latent-class mixed-effect modeling. Multinominal logistic regressions revealed that for individuals with higher CD-RISC scores, greenspace was associated with a greater likelihood of assignment in a resilient trajectory compared with nonremitting high (Wald z test = -3.92; P < .001), nonremitting moderate (Wald z test = -2.24; P = .03), or slow recovery (Wald z test = -2.27; P = .02) classes. Greenspace was also associated with greater neural reactivity to reward in the amygdala (n = 288; t277 = 2.83; adjusted P value = 0.02); however, reward reactivity did not differ by PTSD trajectory.
CONCLUSIONS AND RELEVANCE: In this cohort study, greenspace and self-reported individual resources were significantly associated with PTSD trajectories. These findings suggest that factors at multiple ecological levels may contribute to the likelihood of resiliency to PTSD after trauma.}, }
@article {pmid39082646, year = {2024}, author = {Mallawaarachchi, V and Wickramarachchi, A and Xue, H and Papudeshi, B and Grigson, SR and Bouras, G and Prahl, RE and Kaphle, A and Verich, A and Talamantes-Becerra, B and Dinsdale, EA and Edwards, RA}, title = {Solving genomic puzzles: computational methods for metagenomic binning.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {5}, pages = {}, pmid = {39082646}, issn = {1477-4054}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; DP220102915//Australian Research Council/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Algorithms ; Genomics/methods ; }, abstract = {Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.}, }
@article {pmid39082518, year = {2024}, author = {Cabral, BVB and Sousa, GJB and Cordeiro, LI and Maranhão, TA and Pereira, MLD}, title = {Temporal Pattern and Spatial Distribution of Tuberculosis Prevalence Associated with Multimorbidity in Brazil.}, journal = {Revista da Sociedade Brasileira de Medicina Tropical}, volume = {57}, number = {}, pages = {e00408}, pmid = {39082518}, issn = {1678-9849}, mesh = {Humans ; Brazil/epidemiology ; Prevalence ; *Tuberculosis/epidemiology ; *Spatio-Temporal Analysis ; Male ; *Multimorbidity ; Female ; Adult ; Middle Aged ; Chronic Disease/epidemiology ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Four main chronic conditions may be involved in the tuberculosis pathogenic process and/or clinical evolution: HIV/AIDS, diabetes mellitus, mental illness, and Chronic Obstructive Pulmonary Disease. This study aimed to determine the spatiotemporal pattern of tuberculosis (TB) associated with multimorbidity in Brazil.
METHODS: Ecological study use data from the Notifiable Diseases Information System (SINAN), collected from the electronic portal of the Department of Informatics of the SUS (DATASUS). These data included TB cases that were reported between 2007 and 2021 and were associated with two or more chronic clinical health conditions (multimorbidity).
RESULTS: A total of 7,795 cases of TB associated with multimorbidity were recorded, with an average growth trend of 4.6% per year (95% Confidence Interval (CI): 3.3-5.9; p<0.001) and higher growth in the first temporal segment (2007 to 2011) (8.9%; 95%CI: 4.2-13.9; p=0.002). The spatial analysis, after Bayesian smoothing, highlighted the main municipalities states of the study, namely: São Paulo (19.8%; n = 297), Porto Alegre (23.6%; n = 354), and Rio de Janeiro (44.8%; n = 672). The proportion of extremely poor (β=-0.002), the bolsa família program (β=0.002), the average per-person income (β=0.001), and the percentage of the population living in households with a density of more than 2 people per bedroom (β=0.001) were related to chronic health conditions.
CONCLUSIONS: These findings will stimulate public action to manage this situation. However, as this is still a recent topic in the literature, we encourage the development of studies on the synergistic characteristics of TB and other clinical conditions.}, }
@article {pmid39082244, year = {2024}, author = {Farrell, MJ and Le Guillarme, N and Brierley, L and Hunter, B and Scheepens, D and Willoughby, A and Yates, A and Mideo, N}, title = {The changing landscape of text mining: a review of approaches for ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2027}, pages = {20240423}, pmid = {39082244}, issn = {1471-2954}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Data Mining ; *Ecology/methods ; *Biological Evolution ; *Natural Language Processing ; Machine Learning ; }, abstract = {In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.}, }
@article {pmid39081076, year = {2024}, author = {Levy, O and Shahar, S}, title = {Artificial Intelligence for Climate Change Biology: From Data Collection to Predictions.}, journal = {Integrative and comparative biology}, volume = {64}, number = {3}, pages = {953-974}, doi = {10.1093/icb/icae127}, pmid = {39081076}, issn = {1557-7023}, support = {300/22//Israeli Science Foundation/ ; NGS-84241T-21//National Geographic Society/ ; IOS-1754949//National Science Foundation/ ; }, mesh = {*Climate Change ; *Artificial Intelligence ; Animals ; Big Data ; Microclimate ; Data Collection/methods ; }, abstract = {In the era of big data, ecological research is experiencing a transformative shift, yet big-data advancements in thermal ecology and the study of animal responses to climate conditions remain limited. This review discusses how big data analytics and artificial intelligence (AI) can significantly enhance our understanding of microclimates and animal behaviors under changing climatic conditions. We explore AI's potential to refine microclimate models and analyze data from advanced sensors and camera technologies, which capture detailed, high-resolution information. This integration can allow researchers to dissect complex ecological and physiological processes with unprecedented precision. We describe how AI can enhance microclimate modeling through improved bias correction and downscaling techniques, providing more accurate estimates of the conditions that animals face under various climate scenarios. Additionally, we explore AI's capabilities in tracking animal responses to these conditions, particularly through innovative classification models that utilize sensors such as accelerometers and acoustic loggers. For example, the widespread usage of camera traps can benefit from AI-driven image classification models to accurately identify thermoregulatory responses, such as shade usage and panting. AI is therefore instrumental in monitoring how animals interact with their environments, offering vital insights into their adaptive behaviors. Finally, we discuss how these advanced data-driven approaches can inform and enhance conservation strategies. In particular, detailed mapping of microhabitats essential for species survival under adverse conditions can guide the design of climate-resilient conservation and restoration programs that prioritize habitat features crucial for biodiversity resilience. In conclusion, the convergence of AI, big data, and ecological science heralds a new era of precision conservation, essential for addressing the global environmental challenges of the 21st century.}, }
@article {pmid39080706, year = {2024}, author = {Hamamoto, K and Mizuyama, M and Nishijima, M and Maeda, A and Gibu, K and Poliseno, A and Iguchi, A and Reimer, JD}, title = {Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {54}, pmid = {39080706}, issn = {2524-6372}, support = {20H00653//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.
RESULTS: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.
CONCLUSION: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.}, }
@article {pmid39079269, year = {2024}, author = {Tian, Y and Liu, Y and Yue, L and Zhao, X and Zhou, Q and Uwaremwe, C and Wang, Y and Chen, G and Sha, Y and Zhang, Y and Wang, R}, title = {Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.}, journal = {Microbiological research}, volume = {287}, number = {}, pages = {127855}, doi = {10.1016/j.micres.2024.127855}, pmid = {39079269}, issn = {1618-0623}, mesh = {*Solanum tuberosum/microbiology/growth & development ; *Fertilizers/analysis ; *Soil Microbiology ; Bacillus amyloliquefaciens/growth & development ; Transcriptome ; Plant Tubers/microbiology/growth & development ; Microbiota ; Soil/chemistry ; Metabolome ; Rhizosphere ; Sucrose/metabolism ; Plant Development ; Metabolomics/methods ; Multiomics ; }, abstract = {Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.}, }
@article {pmid39075558, year = {2024}, author = {Pinheiro-Junior, EL and Alirahimi, E and Peigneur, S and Isensee, J and Schiffmann, S and Erkoc, P and Fürst, R and Vilcinskas, A and Sennoner, T and Koludarov, I and Hempel, BF and Tytgat, J and Hucho, T and von Reumont, BM}, title = {Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {164}, pmid = {39075558}, issn = {1741-7007}, support = {2016/04761-4//São Paulo Research Foundation/ ; GOC2319 N//F.W.O.-Vlaanderen/ ; GOA4919 N//F.W.O.-Vlaanderen/ ; G0E7120N//F.W.O.-Vlaanderen/ ; PDM/19/164//KU Leuven funding/ ; CA19144 EUVEN//EU COST Action/ ; }, mesh = {Animals ; *Potassium Channels/metabolism/genetics ; MAP Kinase Signaling System/drug effects ; Phylogeny ; Mice ; Cyclic AMP-Dependent Protein Kinases/metabolism/genetics ; Evolution, Molecular ; Humans ; Arthropod Venoms/chemistry ; }, abstract = {BACKGROUND: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.
RESULTS: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13 with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing, we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.
CONCLUSIONS: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.}, }
@article {pmid39074140, year = {2024}, author = {Melo, D and Pallares, LF and Ayroles, JF}, title = {Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.}, journal = {PLoS computational biology}, volume = {20}, number = {7}, pages = {e1012300}, pmid = {39074140}, issn = {1553-7358}, support = {R01 ES029929/ES/NIEHS NIH HHS/United States ; R35 GM124881/GM/NIGMS NIH HHS/United States ; }, mesh = {*Drosophila melanogaster/genetics ; Animals ; *Gene Regulatory Networks/genetics ; *Stochastic Processes ; *Algorithms ; *Computational Biology/methods ; Models, Genetic ; Gene Expression Profiling/methods ; }, abstract = {Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNAseq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.}, }
@article {pmid39071792, year = {2023}, author = {Falk, S and Gorše, I and , and , and , and , and , and , }, title = {The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {311}, pmid = {39071792}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.}, }
@article {pmid39069513, year = {2024}, author = {Xu, R and Xu, C and Li, Z and Zheng, T and Yu, W and Yang, C}, title = {Boundary guidance network for medical image segmentation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17345}, pmid = {39069513}, issn = {2045-2322}, support = {2019YFC0117800//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Image Processing, Computer-Assisted/methods ; Deep Learning ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Algorithms ; Cystoscopy/methods ; Image Interpretation, Computer-Assisted/methods ; }, abstract = {Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.}, }
@article {pmid39068884, year = {2024}, author = {Fan, Q and Huang, S and Guo, J and Xie, Y and Chen, M and Chen, Y and Qi, W and Liu, H and Jia, Z and Hu, H and Qu, J}, title = {Spatiotemporal distribution and transport flux of organophosphate esters in the sediment of the Yangtze River.}, journal = {Journal of hazardous materials}, volume = {477}, number = {}, pages = {135312}, doi = {10.1016/j.jhazmat.2024.135312}, pmid = {39068884}, issn = {1873-3336}, abstract = {The Yangtze River Basin is an important area for organophosphate esters (OPEs) consumption and emission. Studies proved high OPE detection in Yangtze River water, but there is limited information about the spatiotemporal distribution and transport flux of OPEs in sediment. The present study investigated 16 OPEs in sediment from upstream to mid-downstream of the Yangtze River. The mean concentration of OPEs was 84.30 ng/g, and alkyl-OPEs was the primary component. Great specific surface area and high content of organic carbon significantly increased OPE concentration in Three Gorges Reservoir (TGR) by physical adsorption and chemical bonds (p < 0.05), making TGR the most contaminated area in mainstream. No significant differences in OPE constituents were found in seasonal distribution. Four potential sources of OPEs were identified by principal component analysis and self-organizing maps, and traffic emissions were the dominant source for OPEs. The hazard quotient model results indicated that aryl-OPEs showed moderate risks in the mainstream of Yangtze River, alkyl-OPEs and Cl-OPEs showed low risks. TGR was a significant sink of OPEs in Yangtze River and buried 7.41 tons of OPEs in 2020, a total of 14.87 tons of OPE were transported into the sea by sediment.}, }
@article {pmid39066932, year = {2024}, author = {Seldeslachts, A and Maurstad, MF and Øyen, JP and Undheim, EAB and Peigneur, S and Tytgat, J}, title = {Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {81}, number = {1}, pages = {311}, pmid = {39066932}, issn = {1420-9071}, support = {GOC2319N, GOA4919N, and G0E7120N//Fonds Wetenschappelijk Onderzoek/ ; 12W7822N//Fonds Wetenschappelijk Onderzoek/ ; 1S51521N and 1S51523N//Fonds Wetenschappelijk Onderzoek/ ; CA19144 EUVEN//European Cooperation in Science and Technology/ ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/ ; 101039862//H2020 European Research Council/ ; }, mesh = {Animals ; *Proteomics/methods ; *Transcriptome ; *Moths/genetics ; Arthropod Venoms ; Larva/metabolism ; Quercus ; Gene Expression Profiling ; Allergens/immunology ; Insect Proteins/genetics/metabolism ; Proteome/metabolism ; Computational Biology/methods ; }, abstract = {Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.}, }
@article {pmid39060281, year = {2024}, author = {Khaki, JJ and Meiring, JE and Thindwa, D and Henrion, MYR and Jere, TM and Msuku, H and , and Heyderman, RS and Gordon, MA and Giorgi, E}, title = {Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17164}, pmid = {39060281}, issn = {2045-2322}, support = {106158/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 617 OPP1141321//Bill and Melinda Gates Foundation/ ; }, mesh = {Humans ; *Typhoid Fever/epidemiology/microbiology ; *Salmonella typhi/isolation & purification ; Adolescent ; Child ; Malawi/epidemiology ; Adult ; Child, Preschool ; Male ; Female ; Young Adult ; Incidence ; Infant ; Risk Factors ; Sanitation ; Urban Population ; }, abstract = {Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.}, }
@article {pmid39060268, year = {2024}, author = {Tagliaferro, S and Maio, S and Pirona, F and Stanisci, I and Sarno, G and Silvi, P and Kermenidou, M and Papaioannou, N and Perchard, R and Prpic, I and Polanska, K and Jerzynska, J and Ramos, E and Rovira, J and Belmonte, J and Snoj Tratnik, JS and Horvat, M and Kocman, D and Spiric, Z and Zickella, J and Fasola, S and La Grutta, S and Malizia, V and Montalbano, L and , and , and Baldacci, S and Annesi-Maesano, I}, title = {Assessing external exposome by implementing an Environmental Data Management System using Open Data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {17142}, pmid = {39060268}, issn = {2045-2322}, support = {603946//European Commission/ ; }, mesh = {Humans ; Male ; Female ; *Exposome ; Environmental Exposure ; Data Management ; Environmental Monitoring/methods ; Europe ; Aged, 80 and over ; Cities ; Aged ; }, abstract = {Due to the increasing importance of exposome in environmental epidemiology, feasibility and usefulness of an Environmental Data Management System (EDMS) using Open Data was evaluated. The EDMS includes data from 10 European cities (Celje (Slovenia), Łódź (Poland), Manchester (UK), Palermo (Italy), Paris (France), Porto (Portugal), Regensburg (Germany), Reus (Spain), Rijeka (Croatia), Thessaloniki (Greece)) about external non-specific and specific exposome factors at the city or country level (2017-2020). Findings showed that the highest values of life expectancy were in Reus females (86 years) and Palermo males (81 years). UK had the highest obesity rate (28%), Croatia the highest prescribed drug consumption (62%), Greece and Portugal the highest smoking rates (37%, 42%) and daily alcohol consumption (21%), respectively. The most polluted cities were Thessaloniki for PM10 (38 µg/m[3]), Łódź for PM2.5 (25 µg/m[3]), Porto for NO2 (62 µg/m[3]) and Rijeka for O3 (92 µg/m[3]). Thessaloniki had the highest grey space (98%) and Łódź the highest cumulative amount of pollen (39,041 p/m[3]). The highest daily noise levels ≥ 55 dB was in Reus (81% to traffic) and Regensburg (21% to railway). In drinking water, arsenic had the highest value in Thessaloniki (6.4 µg/L), boron in Celje (24 mg/L) and lead in Paris (46.7 µg/L). Portugal and Greece showed the highest pesticide residues in food (7%). In conclusion, utilizing open-access databases enables the translation of research findings into actionable strategies for public health interventions.}, }
@article {pmid39059890, year = {2024}, author = {Tikhomirov, L and Semmler, C and McCradden, M and Searston, R and Ghassemi, M and Oakden-Rayner, L}, title = {Medical artificial intelligence for clinicians: the lost cognitive perspective.}, journal = {The Lancet. Digital health}, volume = {6}, number = {8}, pages = {e589-e594}, doi = {10.1016/S2589-7500(24)00095-5}, pmid = {39059890}, issn = {2589-7500}, mesh = {*Artificial Intelligence ; Humans ; *Clinical Decision-Making/methods ; Cognition ; Decision Support Systems, Clinical ; Radiology ; }, abstract = {The development and commercialisation of medical decision systems based on artificial intelligence (AI) far outpaces our understanding of their value for clinicians. Although applicable across many forms of medicine, we focus on characterising the diagnostic decisions of radiologists through the concept of ecologically bounded reasoning, review the differences between clinician decision making and medical AI model decision making, and reveal how these differences pose fundamental challenges for integrating AI into radiology. We argue that clinicians are contextually motivated, mentally resourceful decision makers, whereas AI models are contextually stripped, correlational decision makers, and discuss misconceptions about clinician-AI interaction stemming from this misalignment of capabilities. We outline how future research on clinician-AI interaction could better address the cognitive considerations of decision making and be used to enhance the safety and usability of AI models in high-risk medical decision-making contexts.}, }
@article {pmid39057817, year = {2024}, author = {Chanda, MM and Purse, BV and Sedda, L and Benz, D and Prasad, M and Reddy, YN and Yarabolu, KR and Byregowda, SM and Carpenter, S and Prasad, G and Rogers, DJ}, title = {Bluetongue Risk Map for Vaccination and Surveillance Strategies in India.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {39057817}, issn = {2076-0817}, support = {BB/H009167/1//BBSRC, DFID, Scottish government/ ; }, abstract = {Bluetongue virus (BTV, Sedoreoviridae: Orbivirus) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges (Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.}, }
@article {pmid39056317, year = {2024}, author = {Stulberg, EL and Lisabeth, L and Schneider, ALC and Skolarus, L and Kershaw, KN and Zheutlin, AR and Harris, BRE and Sarpong, D and Wong, KH and Sheth, KN and de Havenon, A}, title = {Correlations of Socioeconomic and Clinical Determinants with United States County-Level Stroke Prevalence.}, journal = {Annals of neurology}, volume = {96}, number = {4}, pages = {739-744}, doi = {10.1002/ana.27039}, pmid = {39056317}, issn = {1531-8249}, support = {R01 NS107463/NH/NIH HHS/United States ; 1R38HL167282-01/HI/NHLBI NIH HHS/United States ; R01MD016178/NS/NINDS NIH HHS/United States ; R01NS110721/NS/NINDS NIH HHS/United States ; HT9425-23-1-0981//Department of Defense/ ; R01 HL152741/NH/NIH HHS/United States ; R01 HL156906/NH/NIH HHS/United States ; //American Heart Association/American Stroke Association/ ; U24NS107136/NS/NINDS NIH HHS/United States ; R01EB301114/NS/NINDS NIH HHS/United States ; R01NR018335/NS/NINDS NIH HHS/United States ; /MD/NIMHD NIH HHS/United States ; /AG/NIA NIH HHS/United States ; R01NS130189/NS/NINDS NIH HHS/United States ; U24NS129500/NS/NINDS NIH HHS/United States ; W81XWH-21-1-0590//Department of Defense/ ; K23NS123340/NS/NINDS NIH HHS/United States ; R38 HL167282/HL/NHLBI NIH HHS/United States ; U24NS107215/NS/NINDS NIH HHS/United States ; R01 NS038916/NH/NIH HHS/United States ; U01NS106513/NS/NINDS NIH HHS/United States ; UG3NS130228/NS/NINDS NIH HHS/United States ; K23NS105924/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Stroke/epidemiology ; United States/epidemiology ; Prevalence ; Socioeconomic Factors ; Risk Factors ; Social Class ; Male ; Female ; Adult ; Middle Aged ; Health Services Accessibility ; Aged ; }, abstract = {Socioeconomic status (SES) is a multi-faceted theoretical construct associated with stroke risk and outcomes. Knowing which SES measures best correlate with population stroke metrics would improve its accounting in observational research and inform interventions. Using the Centers for Disease Control and Prevention's (CDC) Population Level Analysis and Community Estimates (PLACES) and other publicly available databases, we conducted an ecological study comparing correlations of different United States county-level SES, health care access and clinical risk factor measures with age-adjusted stroke prevalence. The prevalence of adults living below 150% of the federal poverty level most strongly correlated with stroke prevalence compared to other SES and non-SES measures (correlation coefficient = 0.908, R[2] = 0.825; adjusted partial correlation coefficient: 0.589, R[2] = 0.347). ANN NEUROL 2024;96:739-744.}, }
@article {pmid39056051, year = {2024}, author = {Navarro-Farfán, MDM and García-Romero, L and Martínez-Cinco, MA and Domínguez-Sánchez, C and Sánchez-Quispe, ST}, title = {Methodology for the assessment of poor-data water resources.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17755}, pmid = {39056051}, issn = {2167-8359}, mesh = {*Water Resources ; Models, Theoretical ; Hydrology/methods ; Environmental Monitoring/methods ; }, abstract = {Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented.}, }
@article {pmid39053536, year = {2024}, author = {He, M and Cui, J and Yi, Y and Chen, HW and Zhang, Q and Li, L and Huang, L and Hong, S}, title = {Vegetation increases global climate vulnerability risk by shifting climate zones in response to rising atmospheric CO2.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174810}, doi = {10.1016/j.scitotenv.2024.174810}, pmid = {39053536}, issn = {1879-1026}, mesh = {*Carbon Dioxide/analysis ; *Climate Change ; *Ecosystem ; Atmosphere/chemistry ; }, abstract = {Global climate zones are experiencing widespread shifts with ongoing rise in atmospheric CO2, influencing vegetation growth and shifting its distributions to challenge ecosystem structure and function, posing threats on ecological and societal safety. However, how rising atmospheric CO2 affects the pace of global climate zone shifts is highly uncertain. More attentions are urgently required to understand the underlying mechanisms and quantifications of regional climate vulnerability in response to rising CO2. In this study, we employ nine Earth system models from CMIP6 to investigate global climate zone shifts with rising CO2, unravel the effects of vegetation physiological response (PHY), and categorize climate vulnerable regions depending on the extent of climate zone shifts. We find that climate zone shifts over half of the global land area, 16.8% of which is contributed by PHY at 4 × CO2. Intriguingly, besides warming, PHY-induced precipitation changes and their interactions with warming dominate about two-fifths of PHY-forced shifts, providing potential direction for model improvement in future predictions of climate zone shifts. Aided with PHY effects, 4 × CO2 imposes substantial climate zone shifts over about one-fifth of the global land area, suggesting substantial changes in local climate and ecosystem structure and functions. Hence, those regions would experience strong climate vulnerability, and face high risk of climate extremes, water scarcity and food production. Our results quantitatively identify the vulnerable regions and unravel the underlying drivers, providing scientific insights to prioritize conservation and restoration efforts to ensure ecological and social safety globally.}, }
@article {pmid39051209, year = {2024}, author = {de Souza, OF and Araújo, ACB and Vieira, LB and Bachur, JA and Lopez, AGP and Gonçalves, TG and de Abreu, LC}, title = {Sex Disparity in Stroke Mortality among Adults: A Time Series Analysis in the Greater Vitoria Region, Brazil (2000-2021).}, journal = {Epidemiologia (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {402-410}, pmid = {39051209}, issn = {2673-3986}, abstract = {The disparity between the sexes in stroke mortality has been demonstrated in people from different locations. The objective of this study was to analyze the disparity between sexes in stroke mortality in adults in the metropolitan area of Greater Vitoria between 2000 and 2021. Ecological time series design was conducted with a database of the Brazilian Health System Informatics Department. The annual percentage change and average annual percentage change were calculated through joinpoint regression. Pairwise comparisons using parallelism and coincidence tests were applied to compare temporal trends between men and women. Men had higher mortality rates in most years between 2000 and 2021. In contrast, women had higher proportional mortality values in all years evaluated from 2000 to 2021. The paired comparison revealed a disparity between the sexes in the proportional mortality time series (parallelism test: p = 0.003; coincidence test: p < 0.001). However, the time series of the mortality rates showed no disparity between the sexes (parallelism test: p = 0.114; coincidence test: p = 0.093). From 2000 to 2021, there was a disparity in proportional mortality from stroke between the sexes of the population in the metropolitan area of Greater Vitoria, Brazil. However, the time series of mortality rates between the sexes did not reveal any disparity in the study period.}, }
@article {pmid39050029, year = {2024}, author = {Kryukov, K and Nakahama, N and Kuraku, S}, title = {Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {583}, pmid = {39050029}, issn = {2046-1402}, mesh = {Animals ; *Biodiversity ; *Endangered Species ; Genome ; *Genomics/methods ; Japan ; }, abstract = {Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.}, }
@article {pmid39049113, year = {2024}, author = {Yurkov, A and Visagie, CM and Crous, PW and Hashimoto, A and Baschien, C and Begerow, D and Kemler, M and Schoutteten, N and Stadler, M and Wijayawardene, NN and Hyde, KD and Zhang, N and Boekhout, T and , and May, TW and Thines, M and Hawksworth, DL}, title = {Cultures as types and the utility of viable specimens for fungal nomenclature.}, journal = {IMA fungus}, volume = {15}, number = {1}, pages = {20}, pmid = {39049113}, issn = {2210-6340}, abstract = {The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.}, }
@article {pmid39048683, year = {2024}, author = {Gauci, V and Pangala, SR and Shenkin, A and Barba, J and Bastviken, D and Figueiredo, V and Gomez, C and Enrich-Prast, A and Sayer, E and Stauffer, T and Welch, B and Elias, D and McNamara, N and Allen, M and Malhi, Y}, title = {Global atmospheric methane uptake by upland tree woody surfaces.}, journal = {Nature}, volume = {631}, number = {8022}, pages = {796-800}, pmid = {39048683}, issn = {1476-4687}, mesh = {*Atmosphere/chemistry ; *Forests ; *Methane/metabolism/analysis ; Taiga ; *Trees/chemistry/metabolism/microbiology ; Tropical Climate ; *Wood/chemistry/metabolism/microbiology ; Greenhouse Gases/analysis/metabolism ; Carbon Isotopes ; Forestry ; Global Warming/prevention & control/statistics & numerical data ; Greenhouse Effect/prevention & control/statistics & numerical data ; }, abstract = {Methane is an important greenhouse gas[1], but the role of trees in the methane budget remains uncertain[2]. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base[3,4], it has also been suggested that upland trees can serve as a net sink for atmospheric methane[5,6]. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.}, }
@article {pmid39048062, year = {2024}, author = {Kondak, S and Kondak, D and Kabadayi, O and Erdei, L and Rónavári, A and Kónya, Z and Galbács, G and Kolbert, Z}, title = {Current insights into the green synthesis, in planta characterization and phytoeffects of nickel nanoparticles and their agricultural implications.}, journal = {Environmental research}, volume = {260}, number = {}, pages = {119665}, doi = {10.1016/j.envres.2024.119665}, pmid = {39048062}, issn = {1096-0953}, mesh = {*Nickel/toxicity ; *Metal Nanoparticles/toxicity ; Plants/drug effects ; Agriculture ; Green Chemistry Technology ; }, abstract = {The intensifying production and release into the environment as well as the increasing potential in agricultural applications make the relationship between plants and nickel nanoparticles (Ni NPs) a relevant and timely topic. The aim of this review is to give an overview and discuss the latest findings about the relationship of Ni NPs and plants. Ni NPs can be synthesized using phytochemicals derived from plant parts in an environmentally friendly manner. There are several ways for these nanoparticles to enter plant cells and tissues. This can be demonstrated through various imaging and chemical mapping approaches (e.g., transmission electron microscopy, X-ray fluorescence spectroscopy etc.). NiO NPs affect plants at multiple levels, including subcellular, cellular, tissue, organ, and whole-plant levels. However, the effects of Ni NPs on plants' ecological partners (e.g., rhizobiome, pollinators) remain largely unknown despite their ecotoxicological significance. The main cause of the Ni NPs-triggered damages is the reactive oxygen species imbalance as a consequence of the modulation of antioxidants. In non-tolerant plants, the toxicity of NiO NPs can be mitigated by exogenous treatments such as the application of silicon, salicylic acid, or jasmonic acid, which induce defense mechanisms whereas Ni-hypertolerant plant species possess endogenous defense systems, such as cell wall modifications and nitrosative signaling against NiO NP stress. Research highlights the role of Ni NPs in managing fungal diseases, showcasing their antifungal properties against specific pathogens. Due to the essentiality of Ni, the application of Ni NPs as nanofertilizers might be promising and has recently started to come into view.}, }
@article {pmid39047578, year = {2024}, author = {Maxion, A and Gaebler, AJ and Röhrig, R and Mathiak, K and Zweerings, J and Kutafina, E}, title = {Spectral changes in electroencephalography linked to neuroactive medications: A computational pipeline for data mining and analysis.}, journal = {Computer methods and programs in biomedicine}, volume = {255}, number = {}, pages = {108319}, doi = {10.1016/j.cmpb.2024.108319}, pmid = {39047578}, issn = {1872-7565}, mesh = {Humans ; *Electroencephalography/methods ; *Data Mining/methods ; Carbamazepine/therapeutic use/pharmacology ; Risperidone ; Antipsychotic Agents/pharmacology ; Anticonvulsants/pharmacology/therapeutic use ; Brain/drug effects ; }, abstract = {BACKGROUND AND OBJECTIVES: The increasing amount of open-access medical data provides new opportunities to gain clinically relevant information without recruiting new patients. We developed an open-source computational pipeline, that utilizes the publicly available electroencephalographic (EEG) data of the Temple University Hospital to identify EEG profiles associated with the usage of neuroactive medications. It facilitates access to the data and ensures consistency in data processing and analysis, thus reducing the risk of errors and creating comparable and reproducible results. Using this pipeline, we analyze the influence of common neuroactive medications on brain activity.
METHODS: The pipeline is constructed using easily controlled modules. The user defines the medications of interest and comparison groups. The data is downloaded and preprocessed, spectral features are extracted, and statistical group comparison with visualization through a topographic EEG map is performed. The pipeline is adjustable to answer a variety of research questions. Here, the effects of carbamazepine and risperidone were statistically compared with control data and with other medications from the same classes (anticonvulsants and antipsychotics).
RESULTS: The comparison between carbamazepine and the control group showed an increase in absolute and relative power for delta and theta, and a decrease in relative power for alpha, beta, and gamma. Compared to antiseizure medications, carbamazepine showed an increase in alpha and theta for absolute powers, and for relative powers an increase in alpha and theta, and a decrease in gamma and delta. Risperidone compared with the control group showed a decrease in absolute and relative power for alpha and beta and an increase in theta for relative power. Compared to antipsychotic medications, risperidone showed a decrease in delta for absolute powers. These results show good agreement with state-of-the-art research. The database allows to create large groups for many different medications. Additionally, it provides a collection of records labeled as "normal" after expert assessment, which is convenient for the creation of control groups.
CONCLUSIONS: The pipeline allows fast testing of different hypotheses regarding links between medications and EEG spectrum through ecological usage of readily available data. It can be utilized to make informed decisions about the design of new clinical studies.}, }
@article {pmid39045996, year = {2024}, author = {Lima, AGCF and Ribeiro, CJN and Lima, SVMA and Barbosa, YM and Oliveira, IM and Araújo, KCGM}, title = {Space-time analysis of work-related musculoskeletal disorders in Brazil: an ecological study.}, journal = {Cadernos de saude publica}, volume = {40}, number = {7}, pages = {e00141823}, pmid = {39045996}, issn = {1678-4464}, mesh = {Humans ; Brazil/epidemiology ; *Musculoskeletal Diseases/epidemiology ; *Occupational Diseases/epidemiology ; *Spatio-Temporal Analysis ; Incidence ; Male ; Female ; Bayes Theorem ; Risk Factors ; Adult ; }, abstract = {This study aimed to analyze the incidence of work-related musculoskeletal disorders (WMSD) in Brazil from 2007 to 2019, examining the spatial, temporal, and spatiotemporal patterns of their occurrence. An ecological time series study was conducted using spatial analysis techniques. WMSD morbidity data from 2007 to 2019 were collected from the Brazilian Information System for Notificable Diseases of the Brazilian Health Informatics Department. Incidence rates were standardized and smoothed using the local empirical Bayes' theorem. Time trends were analyzed by segmented linear regression. Spatial analysis was performed using Moran's univariate global (I) and local (LISA) indexes. The spatiotemporal scan statistic was used to identify high-risk spatiotemporal clusters for WMSD. A total of 93,387 cases of WMSD were recorded in Brazil. Temporal trends showed an increase in all regions except the Northeast, which remained stable. The incidence of WMSD showed a spatial dependence, with spatial and space-time clusters identified, especially in the Southeast region, overlapping the largest economic-industrial center of the country. The spatiotemporal clustering observed in one region suggests the highest level of industrial and economic development. Our findings highlight the need to implement intersectoral surveillance policies, inspect working conditions, and invest in the prevention and promotion of workers' health.}, }
@article {pmid39045504, year = {2024}, author = {Märtz, J and Tallian, A and Wikenros, C and Heeres, RW}, title = {"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.}, journal = {Ecology and evolution}, volume = {14}, number = {7}, pages = {e11695}, pmid = {39045504}, issn = {2045-7758}, abstract = {The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).}, }
@article {pmid39032255, year = {2024}, author = {Hossain, M and Wiegand, B and Reza, A and Chaudhuri, H and Mukhopadhyay, A and Yadav, A and Patra, PK}, title = {A machine learning approach to investigate the impact of land use land cover (LULC) changes on groundwater quality, health risks and ecological risks through GIS and response surface methodology (RSM).}, journal = {Journal of environmental management}, volume = {366}, number = {}, pages = {121911}, doi = {10.1016/j.jenvman.2024.121911}, pmid = {39032255}, issn = {1095-8630}, mesh = {*Groundwater/analysis ; *Machine Learning ; *Water Quality ; *Geographic Information Systems ; India ; Environmental Monitoring/methods ; Bayes Theorem ; Humans ; Agriculture ; }, abstract = {Groundwater resources are enormously affected by land use land cover (LULC) dynamics caused by increasing urbanisation, agricultural and household discharge as a result of global population growth. This study investigates the impact of decadal LULC changes in groundwater quality, human and ecological health from 2009 to 2021 in a diverse landscape, West Bengal, India. Using groundwater quality data from 479 wells in 2009 and 734 well in 2021, a recently proposed Water Pollution Index (WPI) was computed, and its geospatial distribution by a machine learning-based 'Empirical Bayesian Kriging' (EBK) tool manifested a decline in water quality since the number of excellent water category decreased from 30.5% to 28% and polluted water increased from 44% to 45%. ANOVA and Friedman tests revealed statistically significant differences (p < 0.0001) in year-wise water quality parameters as well as group comparisons for both years. Landsat 7 and 8 satellite images were used to classify the LULC types applying machine learning tools for both years, and were coupled with response surface methodology (RSM) for the first time, which revealed that the alteration of groundwater quality were attributed to LULC changes, e.g. WPI showed a positive correlation with built-up areas, village-vegetation cover, agricultural lands, and a negative correlation with surface water, barren lands, and forest cover. Expansion in built-up areas by 0.7%, and village-vegetation orchards by 2.3%, accompanied by a reduction in surface water coverage by 0.6%, and 2.4% in croplands caused a 1.5% drop in excellent water and 1% increase in polluted water category. However, ecological risks through the ecological risk index (ERI) exhibited a lower risk in 2021 attributed to reduced high-risk potential zones. This study highlights the potentiality in linking LULC and water quality changes using some advanced statistical tools like GIS and RSM for better management of water quality and landscape ecology.}, }
@article {pmid39032150, year = {2024}, author = {Kim, J and Foo, JC and Murata, T and Togo, F}, title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.}, journal = {Stress and health : journal of the International Society for the Investigation of Stress}, volume = {40}, number = {5}, pages = {e3447}, doi = {10.1002/smi.3447}, pmid = {39032150}, issn = {1532-2998}, support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Humans ; *Heart Rate/physiology ; *Stress, Psychological/physiopathology/psychology ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Affect/physiology ; Exercise/psychology/physiology ; }, abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.}, }
@article {pmid39031697, year = {2024}, author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC}, title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.}, journal = {Medical and veterinary entomology}, volume = {38}, number = {4}, pages = {375-392}, doi = {10.1111/mve.12733}, pmid = {39031697}, issn = {1365-2915}, support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Anopheles/physiology ; Malawi ; *Seasons ; *Mosquito Vectors/physiology ; *Malaria/transmission ; *Population Density ; Larva/physiology/growth & development ; Female ; }, abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.}, }
@article {pmid39029911, year = {2024}, author = {Tyagi, S and Katara, P}, title = {Metatranscriptomics: A Tool for Clinical Metagenomics.}, journal = {Omics : a journal of integrative biology}, volume = {28}, number = {8}, pages = {394-407}, doi = {10.1089/omi.2024.0130}, pmid = {39029911}, issn = {1557-8100}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; }, abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.}, }
@article {pmid39027808, year = {2024}, author = {Falk, S and Poole, O and , and , and , and , and , and , and , }, title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {74}, pmid = {39027808}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.}, }
@article {pmid39026607, year = {2023}, author = {Boyes, D and Holland, PWH and , and , and , and , and , and , }, title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {303}, pmid = {39026607}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.}, }
@article {pmid39026606, year = {2023}, author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {302}, pmid = {39026606}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.}, }
@article {pmid39026203, year = {2024}, author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L}, title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {669}, pmid = {39026203}, issn = {1479-5876}, support = {RF-2013-02358848//Ministero della Salute/ ; }, mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; }, abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.
METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.
RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift = 2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift = 2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift = 1.97), thyroid dysfunction and AF (lift = 1.75), cerebrovascular disease (CVD)-CAD and AF (lift = 1.55), and hypertension-anemia and CKD (lift = 1.43).
CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.}, }
@article {pmid39024004, year = {2024}, author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S}, title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.}, journal = {JMIR mental health}, volume = {11}, number = {}, pages = {e58352}, pmid = {39024004}, issn = {2368-7959}, support = {R01 DK121298/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; UL1 TR001855/TR/NCATS NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; R01 AG068190/AG/NIA NIH HHS/United States ; U2C AG060408/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; }, abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.
OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.
METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.
RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.
CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.}, }
@article {pmid39023004, year = {2024}, author = {Rillig, MC and Li, C and Rodríguez Del Río, Á and Zhu, YG and Jin, L}, title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17419}, doi = {10.1111/gcb.17419}, pmid = {39023004}, issn = {1365-2486}, support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; }, mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; }, abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.}, }
@article {pmid39018100, year = {2024}, author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A}, title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.}, journal = {JMIR mHealth and uHealth}, volume = {12}, number = {}, pages = {e55094}, pmid = {39018100}, issn = {2291-5222}, mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics & numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics & numerical data/organization & administration ; }, abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.
OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.
METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.
RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.
CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.}, }
@article {pmid39015757, year = {2023}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , }, title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {341}, pmid = {39015757}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.}, }
@article {pmid39015615, year = {2024}, author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , }, title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {65}, pmid = {39015615}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.}, }
@article {pmid39015613, year = {2024}, author = {Obbard, DJ and , and , and , and , and , and , }, title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {56}, pmid = {39015613}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.}, }
@article {pmid39015611, year = {2024}, author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , }, title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {42}, pmid = {39015611}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.}, }
@article {pmid39014019, year = {2024}, author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J}, title = {Cooperation and social organization depend on weighing private and public reputations.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {16443}, pmid = {39014019}, issn = {2045-2322}, mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; }, abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.}, }
@article {pmid39008135, year = {2024}, author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L}, title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {8}, pages = {733}, doi = {10.1007/s10661-024-12886-7}, pmid = {39008135}, issn = {1573-2959}, }
@article {pmid39007251, year = {2024}, author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG}, title = {Forecasting potential invaders to prevent future biological invasions worldwide.}, journal = {Global change biology}, volume = {30}, number = {7}, pages = {e17399}, doi = {10.1111/gcb.17399}, pmid = {39007251}, issn = {1365-2486}, support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; }, mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; }, abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.}, }
@article {pmid39004905, year = {2024}, author = {Herraiz, C and Triguero-Ocaña, R and Laguna, E and Jiménez-Ruiz, S and Peralbo-Moreno, A and Martínez-López, B and García-Bocanegra, I and Risalde, MÁ and Vicente, J and Acevedo, P}, title = {Movement-driven modelling reveals new patterns in disease transmission networks.}, journal = {The Journal of animal ecology}, volume = {93}, number = {9}, pages = {1275-1287}, doi = {10.1111/1365-2656.14142}, pmid = {39004905}, issn = {1365-2656}, support = {PID2019-111699RB-I00//Ministerio de Ciencia e Innovación/ ; AGL2013-48523-C3-1-R//Ministerio de Economía y Competitividad/ ; AGL2016-76358-R//Ministerio de Economía y Competitividad/ ; //European Social Fund/ ; //Government of Castilla-La Mancha/ ; //University of Castilla-La Mancha/ ; }, mesh = {Animals ; Cattle ; Swine ; *Models, Biological ; Spain ; Geographic Information Systems ; Tuberculosis, Bovine/transmission/microbiology ; Swine Diseases/transmission/microbiology ; Movement ; }, abstract = {Interspecific interactions are highly relevant in the potential transmission of shared pathogens in multi-host systems. In recent decades, several technologies have been developed to study pathogen transmission, such as proximity loggers, GPS tracking devices and/or camera traps. Despite the diversity of methods aimed at detecting contacts, the analysis of transmission risk is often reduced to contact rates and the probability of transmission given the contact. However, the latter process is continuous over time and unique for each contact, and is influenced by the characteristics of the contact and the pathogen's relationship with both the host and the environment. Our objective was to assess whether a more comprehensive approach, using a movement-based model which assigns a unique transmission risk to each contact by decomposing transmission into contact formation, contact duration and host characteristics, could reveal disease transmission dynamics that are not detected with more traditional approaches. The model was built from GPS-collar data from two management systems in Spain where animal tuberculosis (TB) circulates: a national park with extensively reared endemic cattle, and an area with extensive free-range pigs and cattle farms. In addition, we evaluated the effect of the GPS device fix rate on the performance of the model. Different transmission dynamics were identified between both management systems. Considering the specific conditions under which each contact occurs (i.e. whether the contact is direct or indirect, its duration, the hosts characteristics, the environmental conditions, etc.) resulted in the identification of different transmission dynamics compared to using only contact rates. We found that fix intervals greater than 30 min in the GPS tracking data resulted in missed interactions, and intervals greater than 2 h may be insufficient for epidemiological purposes. Our study shows that neglecting the conditions under which each contact occurs may result in a misidentification of the real role of each species in disease transmission. This study describes a clear and repeatable framework to study pathogen transmission from GPS data and provides further insights to understand how TB is maintained in multi-host systems in Mediterranean environments.}, }
@article {pmid39004875, year = {2024}, author = {Taylor, A and Sigona, A and Kelly, M}, title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {34}, number = {6}, pages = {e3014}, doi = {10.1002/eap.3014}, pmid = {39004875}, issn = {1051-0761}, support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; }, mesh = {*Grassland ; California ; *Fires ; *Conservation of Natural Resources ; Humans ; Wildfires ; Indigenous Peoples ; }, abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.}, }
@article {pmid39004446, year = {2024}, author = {Fummey, E and Navarro, P and Plazzer, JP and Frayling, IM and Knott, S and Tenesa, A}, title = {Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.}, journal = {Journal of medical genetics}, volume = {61}, number = {9}, pages = {861-869}, pmid = {39004446}, issn = {1468-6244}, mesh = {Humans ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/epidemiology ; Female ; United Kingdom/epidemiology ; *Biological Specimen Banks ; Middle Aged ; *DNA Mismatch Repair/genetics ; *Genetic Predisposition to Disease ; Aged ; Heterozygote ; Exome Sequencing ; Incidence ; Adult ; Breast Neoplasms/genetics/epidemiology ; Endometrial Neoplasms/genetics/epidemiology ; DNA-Binding Proteins/genetics ; MutL Protein Homolog 1/genetics ; UK Biobank ; MutS Homolog 2 Protein ; }, abstract = {UNLABELLED: BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.
METHODS: 830 carriers of pathogenic or likely pathogenic (path_MMR) MMR gene variants classified by InSiGHT were identified in 454 756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).
RESULTS: Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in path_MMR carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in path_MMR carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic PMS2 variants in UKB.
CONCLUSION: These results support offering incidentally identified carriers of any path_MMR surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in MLH1, MSH2 and MSH6 would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.}, }
@article {pmid39004058, year = {2024}, author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H}, title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.}, journal = {Marine pollution bulletin}, volume = {206}, number = {}, pages = {116710}, doi = {10.1016/j.marpolbul.2024.116710}, pmid = {39004058}, issn = {1879-3363}, mesh = {*Seasons ; China ; *Eutrophication ; *Environmental Monitoring ; *Oceans and Seas ; Seawater/chemistry ; Animals ; Temperature ; }, abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze