@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.},
}

Animals
*Butterflies/anatomy & histology/genetics
*Wings, Animal/anatomy & histology
*Neural Networks, Computer
*Sex Characteristics
Male
Female
Species Specificity
Biological Mimicry

@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.},
}

Humans
*Cost-Benefit Analysis
*Decision Making
Epidemiology/education
Geographic Information Systems
Learning

@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.},
}

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

@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.},
}

*Agriculture/methods
*Environmental Monitoring/methods
Crops, Agricultural
Pesticides/analysis
Risk Assessment/methods
Decision Support Techniques
United States
Geographic Information Systems
Ecosystem

@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.},
}

*Butterflies/physiology
Animals
*Animal Distribution
Databases, Factual
Species Specificity
Ecosystem

@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.},
}

*Environmental Monitoring/methods
*Remote Sensing Technology
*Agriculture/methods
*Geographic Information Systems
Crops, Agricultural/growth & development
Seasons

@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.},
}

*Environmental Monitoring/methods
Climate Change
Environment
Europe
Databases, Factual
Industry
Environmental Pollutants/analysis
Environmental Pollution/statistics & numerical data

@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.},
}

*Information Dissemination/methods
Humans
*Computational Biology
Computer Simulation

@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.},
}

*Bryophyta
Chile
*Biodiversity
Antarctic Regions
Ecosystem
Databases, Factual

@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.},
}

*Conservation of Natural Resources/methods
*Ecosystem
China
Humans
Rural Population
Geographic Information Systems

@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.},
}

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

@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.},
}

*Escherichia coli/isolation & purification
Texas
*Internet
Environmental Monitoring/methods
Water Microbiology
Decision Support Techniques

@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.},
}

*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

@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.},
}

*Metabolomics/methods
Chromatography, Liquid/methods
Software
Tandem Mass Spectrometry/methods
Data Interpretation, Statistical

@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.},
}

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

@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 {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.},
}

*Environmental Monitoring/methods
*Ecosystem
*Seasons
Satellite Imagery
Geographic Information Systems

@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.},
}

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

@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.},
}

*Volatile Organic Compounds/metabolism/chemistry
*Bacteria/metabolism/genetics
Microbiota
Metabolomics/methods
Databases, Factual
Humans
Metabolome
Terpenes/metabolism/chemistry
Databases, Chemical

@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.},
}

*Saccharomyces cerevisiae/genetics/metabolism
*Genome, Fungal
*Databases, Genetic
*Genomics/methods
Telomere/genetics
Molecular Sequence Annotation
Proteomics
Multiomics

@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.},
}

Humans
*Semantics
*Attention/physiology
Female
Adult
Male
Young Adult
*Space Perception/physiology
*Visual Perception/physiology
Databases, Factual
Eye-Tracking Technology
Adolescent

@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.},
}

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

@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.},
}

*Ecosystem
*Geographic Information Systems
*Coffea/growth & development
China
Coffee
Climate
Decision Making
Conservation of Natural Resources/methods
Soil/chemistry

@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.},
}

*Lycoris/metabolism/genetics
*Alkaloids/metabolism
Gene Expression Regulation, Plant
Metabolomics
Transcriptome
Soil Microbiology
Protein Interaction Maps
Gene Expression Profiling
Photosynthesis
Metabolome
Genes, Plant
Multiomics

@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.},
}

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

@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.},
}

Humans
Female
*Walking/physiology
Male
Adult
*Geographic Information Systems
*Propensity Score
Middle Aged
Young Adult
Exercise/physiology
Adolescent
Environment Design
Time Factors
Smartphone

@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.},
}

China
*Ecosystem
*Conservation of Natural Resources
*Models, Theoretical
Environmental Monitoring
Forests
Trees/growth & development
Geographic Information Systems

@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.},
}

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

@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.},
}

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

@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.},
}

*Fisheries
Philippines
*Ethnobotany
Humans
*Knowledge
*Conservation of Natural Resources
*Lakes
Ecosystem
Fishes
Animals
Ecology
Female
Male
Middle Aged
Adult
Plants

@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.},
}

Animals
*Periplaneta/metabolism
*Proteomics/methods
*Brain/metabolism
*Insect Proteins/metabolism/analysis
*Proteome
Chromatography, Liquid/methods
Mass Spectrometry/methods
Computational Biology/methods

@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.},
}

*Metadata
*Natural Language Processing
*Machine Learning
Humans
Computational Biology/methods
Proteomics/methods
Vocabulary, Controlled

@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.},
}

*Insecta/microbiology
Animals
*Databases, Factual
*Hypocreales
Host Specificity
Biodiversity

@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.},
}

*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

@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.},
}

*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

@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.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@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.},
}

Animals
*Transcriptome
Fish Venoms/genetics/chemistry
Genomics/methods
Proteomics
Proteome
Alternative Splicing
Fishes/genetics
Phylogeny
Gene Expression Profiling
Multiomics

@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.},
}

Animals
*Animals, Wild
Swine
Swine Diseases
Geographic Information Systems
Humans

@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.},
}

*Ecosystem
Animals
Oceans and Seas
Research/trends
Anthozoa/physiology
Bias
Databases, Factual

@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.},
}

Animals
*Ants/physiology
*Social Behavior
Behavior, Animal/physiology
Models, Biological
Bees/physiology
Computational Biology
Computer Simulation
Social Group

@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.},
}

*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

@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.},
}

*Altitude
*Metabolomics/methods
*Plants/metabolism/genetics
*Proteomics/methods
*Adaptation, Physiological
*Genomics/methods
*Phenotype
Plant Physiological Phenomena
Acclimatization
Transcriptome
Multiomics

@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.},
}

*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

@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.},
}

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

@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.},
}

Animals
*Culicidae/classification
*Deep Learning
*Computational Biology/methods
Entomology/methods
Mosquito Vectors/classification
Humans
Algorithms
Neural Networks, Computer

@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.},
}

*Artificial Intelligence
*Computational Biology
Humans
Cloud Computing/statistics & numerical data
Sustainable Development
Indigenous Peoples/statistics & numerical data
Conservation of Natural Resources

@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.},
}

*Bacteriocins/pharmacology/genetics/metabolism
*Enterobacteriaceae/drug effects/genetics
*Anti-Bacterial Agents/pharmacology
Gram-Negative Bacteria/drug effects/genetics
Plant Diseases/microbiology
Microbial Sensitivity Tests

@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.},
}

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

@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.},
}

*Rainforest
Animals
*Biodiversity
*Vertebrates/physiology
*Conservation of Natural Resources/methods
Tropical Climate
Endangered Species
Ecosystem

@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.},
}

*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

@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.},
}

*Populus/genetics/metabolism
*Coumarins/metabolism
*Polymorphism, Single Nucleotide
*Quantitative Trait Loci
Adaptation, Physiological/genetics
Gene Expression Regulation, Plant
Genes, Plant
Multiomics

@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.},
}

Humans
*Geographic Information Systems
*Ecological Momentary Assessment
Prospective Studies
Male
Adult
Female
Middle Aged
*Mood Disorders/psychology
Smartphone/statistics & numerical data
Affect
Mobile Applications

@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.},
}

*Host-Parasite Interactions/immunology
Animals
Computational Biology
Parasites/physiology/immunology
Immunity, Innate
Models, Biological

@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.},
}

*Computational Biology/methods
Humans
*Microbiota/physiology
*Algorithms
*Gastrointestinal Microbiome/physiology
Microbial Interactions/physiology

@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.},
}

India
*Environmental Monitoring
*Rivers/chemistry
*Geographic Information Systems
Soil Erosion
Conservation of Natural Resources
Hydrology

@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.},
}