@article {pmid39900973,
year = {2025},
author = {Vysakh, VG and Sukumaran, S and Sebastian, W and Gopalakrishnan, A},
title = {The transcriptomic footprint of Mytella strigata: de novo transcriptome assembly of a major invasive species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {201},
pmid = {39900973},
issn = {2052-4463},
mesh = {*Introduced Species ; Animals ; *Transcriptome ; Mytilidae/genetics ; South America ; Gene Ontology ; Molecular Sequence Annotation ; },
abstract = {Mytella strigata, a potentially invasive species native to South America, is rapidly spreading across various aquatic ecosystems around the globe, posing a threat to native mussels. This study presents the first comprehensive de novo transcriptome assembly of M. strigata. We generated 254 million reads, which were processed and assembled using the Trinity assembler, resulting in 60362 transcripts with an N50 of 1,578 bp and over 93-98% completeness, as confirmed by BUSCO analysis with multiple ortho-datasets. A number of databases were used for functional annotation, including UniProt, KEGG, Reactome, InterPro, and eggNOG. Gene Ontology and pathway analyses identified transcripts associated with key biological processes, including those associated with cell signalling, metabolism, stress responses, cancer pathways, and immune regulation. This dataset enriches the bivalve database by advancing the understanding of the adaptive success and evolutionary resilience of this invasive species. The present study provides a fundamental framework for future research on the ecological and evolutionary impacts of this invasive species.},
}

*Introduced Species
Animals
*Transcriptome
Mytilidae/genetics
South America
Gene Ontology
Molecular Sequence Annotation

@article {pmid39899630,
year = {2025},
author = {Sheen, JK and Kennedy-Shaffer, L and Levy, MZ and Metcalf, CJE},
title = {Design of field trials for the evaluation of transmissible vaccines in animal populations.},
journal = {PLoS computational biology},
volume = {21},
number = {2},
pages = {e1012779},
doi = {10.1371/journal.pcbi.1012779},
pmid = {39899630},
issn = {1553-7358},
mesh = {Animals ; *Vaccines/immunology ; Vaccination/methods ; Computational Biology ; Sample Size ; Research Design ; },
abstract = {Vaccines which can transmit from vaccinated to unvaccinated animals may be especially useful for increasing immunity in hard to reach populations or in populations where achieving high coverage is logistically infeasible. However, gauging the public health utility for future use of such transmissible vaccines and assessing their risk-benefit tradeoff, given their potential for unintended evolution, hinges on accurate estimates of their indirect protective effect. Here, we establish the conditions under which a two-stage randomized field trial can characterize the protective effects of a transmissible vaccine relative to a traditional vaccine. We contrast the sample sizes required to adequately power these trials when the vaccine is weakly and strongly transmissible. We also identify how required sample sizes change based on the characteristics of host ecology such as the overdispersion of the contact structure of the population, as well as the efficacy of the vaccine and timing of vaccination. Our results indicate the range of scenarios where two-stage randomized field trial designs are feasible and appropriate to capture the protective effects of transmissible vaccines. Our estimates identify the protective benefit of using transmissible vaccines compared to traditional vaccines, and thus can be used to weigh against evolutionary risks.},
}

Animals
*Vaccines/immunology
Vaccination/methods
Computational Biology
Sample Size
Research Design

@article {pmid39897903,
year = {2025},
author = {Doshi, P and Klas, M and Kyzek, S and Zahoranová, A and Šerá, B},
title = {Investigating the effect of plasma activated water on entomopathogenic nematodes under laboratory conditions.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e42038},
pmid = {39897903},
issn = {2405-8440},
abstract = {Entomopathogenic nematodes are currently being tested for their efficiency in controlling several insect pests. In recent years, non-thermal plasma has been investigated as a state-of-the-art technology for its disinfection/decontamination properties on the seed surface. In addition, it is also used to induce seed germination. In this investigation, the effect of plasma activated water (PAW) was tested on three EPN species, namely Steinernema feltiae Filipjev (1934), S. carpocapsae Weiser (1955), and Heterorhabditis bacteriophora Poinar (1976). Seven different PAW prepared at different treatment times, that is, (1s, 3s, 5s, 10s, 20s, 60s, 90s) were tested directly on the three selected nematode species. Distilled water was used as a control treatment (0s). In the case of H. bacteriophora, significantly higher mortality was observed in PAW preparation times of 5, 10, 20, 60 and 90s compared to the control. In the case of S. feltiae, significantly high mortality was observed for PAW preparation times of 10, 20, 60 and 90s. However, S. carpocapsae was found to have the least sensitivity against all PAW treatments, with a maximum mortality of 14 % (<20 %), indicating the potential synergy between PAW and EPNs. The possibility of combined treatments in the context of integrated pest management is presented and discussed.},
}

@article {pmid39897842,
year = {2025},
author = {Loukili, I and Laamrani, A and El Ghorfi, M and El Moutak, S and Ghafiri, A},
title = {Monitoring land changes at an open mine site using remote sensing and multi-spectral indices.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41845},
pmid = {39897842},
issn = {2405-8440},
abstract = {This study investigates the growth of mining activities in Benguerir, one of Morocco's largest and fastest-growing phosphate mines and a global leader in phosphate production, using remote sensing and ancillary data. The study examines spatio-temporal changes in land use and land cover (LULC) within this phosphate mining city to analyze the impacts of mining on agricultural areas, built-up lands, and water bodies over time. A series of images from 1984 to 2021 were processed in to assess patterns of change within the city. Five LULC maps were generated using supervised classification with the maximum likelihood method, providing detailed insights into both urban and non-urban transformations during the study period. Classification quality was evaluated using accuracy assessment and the Kappa index. Additionally, multi-spectral indices, including the Normalized Difference Vegetation Index (NDVI), Normalized Difference Water Index (NDWI), and Normalized Difference Built-up Index (NDBI), were simulated and analyzed across four intervals. The results reveal significant variations in LULC and ecological indices over time, which are associated with mining activities, water stress, urban sprawl, and socio-economic changes in the region.These results provide a valuable means for decision-makers and planners to effectively manage the spaces and lands in the future.},
}

@article {pmid39897809,
year = {2025},
author = {Milling, M and Rampp, SDN and Triantafyllopoulos, A and Plaza, MP and Brunner, JO and Traidl-Hoffmann, C and Schuller, BW and Damialis, A},
title = {Automating airborne pollen classification: Identifying and interpreting hard samples for classifiers.},
journal = {Heliyon},
volume = {11},
number = {2},
pages = {e41656},
pmid = {39897809},
issn = {2405-8440},
abstract = {Deep-learning-based classification of pollen grains has been a major driver towards automatic monitoring of airborne pollen. Yet, despite an abundance of available datasets, little effort has been spent to investigate which aspects pose the biggest challenges to the (often black-box- resembling) pollen classification approaches. To shed some light on this issue, we conducted a sample-level difficulty analysis based on the likelihood for one of the largest automatically-generated datasets of pollen grains on microscopy images and investigated the reason for which certain airborne samples and specific pollen taxa pose particular problems to deep learning algorithms. It is here concluded that the main challenges lie in A) the (partly) co-occurring of multiple pollen grains in a single image, B) the occlusion of specific markers through the 2D capturing of microscopy images, and C) for some taxa, a general lack of salient, unique features. Our code is publicly available under https://github.com/millinma/SDPollen.},
}

@article {pmid39897501,
year = {2025},
author = {Fuster-Calvo, A and Valentin, S and Tamayo, WC and Gravel, D},
title = {Evaluating the feasibility of automating dataset retrieval for biodiversity monitoring.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18853},
pmid = {39897501},
issn = {2167-8359},
mesh = {*Biodiversity ; *Databases, Factual ; Feasibility Studies ; Information Storage and Retrieval/methods ; Algorithms ; Quebec ; Conservation of Natural Resources/methods ; },
abstract = {AIM: Effective management strategies for conserving biodiversity and mitigating the impacts of global change rely on access to comprehensive and up-to-date biodiversity data. However, manual search, retrieval, evaluation, and integration of this information into databases present a significant challenge to keeping pace with the rapid influx of large amounts of data, hindering its utility in contemporary decision-making processes. Automating these tasks through advanced algorithms holds immense potential to revolutionize biodiversity monitoring.

INNOVATION: In this study, we investigate the potential for automating the retrieval and evaluation of biodiversity data from Dryad and Zenodo repositories. We have designed an evaluation system based on various criteria, including the type of data provided and its spatio-temporal range, and applied it to manually assess the relevance for biodiversity monitoring of datasets retrieved through an application programming interface (API). We evaluated a supervised classification to identify potentially relevant datasets and investigate the feasibility of automatically ranking the relevance. Additionally, we applied the same appraoch on a scientific literature source, using data from Semantic Scholar for reference. Our evaluation centers on the database utilized by a national biodiversity monitoring system in Quebec, Canada.

MAIN CONCLUSIONS: We retrieved 89 (55%) relevant datasets for our database, showing the value of automated dataset search in repositories. Additionally, we find that scientific publication sources offer broader temporal coverage and can serve as conduits guiding researchers toward other valuable data sources. Our automated classification system showed moderate performance in detecting relevant datasets (with an F-score up to 0.68) and signs of overfitting, emphasizing the need for further refinement. A key challenge identified in our manual evaluation is the scarcity and uneven distribution of metadata in the texts, especially pertaining to spatial and temporal extents. Our evaluative framework, based on predefined criteria, can be adopted by automated algorithms for streamlined prioritization, and we make our manually evaluated data publicly available, serving as a benchmark for improving classification techniques.},
}

*Biodiversity
*Databases, Factual
Feasibility Studies
Information Storage and Retrieval/methods
Algorithms
Quebec
Conservation of Natural Resources/methods

@article {pmid39808665,
year = {2025},
author = {Fonseca, LL and Böttcher, L and Mehrad, B and Laubenbacher, RC},
title = {Optimal control of agent-based models via surrogate modeling.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012138},
pmid = {39808665},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; Humans ; Computer Simulation ; Systems Analysis ; Models, Biological ; },
abstract = {This paper describes and validates an algorithm to solve optimal control problems for agent-based models (ABMs). For a given ABM and a given optimal control problem, the algorithm derives a surrogate model, typically lower-dimensional, in the form of a system of ordinary differential equations (ODEs), solves the control problem for the surrogate model, and then transfers the solution back to the original ABM. It applies to quite general ABMs and offers several options for the ODE structure, depending on what information about the ABM is to be used. There is a broad range of applications for such an algorithm, since ABMs are used widely in the life sciences, such as ecology, epidemiology, and biomedicine and healthcare, areas where optimal control is an important purpose for modeling, such as for medical digital twin technology.},
}

*Algorithms
*Computational Biology/methods
Humans
Computer Simulation
Systems Analysis
Models, Biological

@article {pmid39889380,
year = {2025},
author = {Weeks, F and Myerson, R and Gangnon, R and Dykema, J and Cornelius, C and Green, T},
title = {Racial disparities in intrapartum care experiences and birth hospital characteristics.},
journal = {Social science & medicine (1982)},
volume = {367},
number = {},
pages = {117720},
doi = {10.1016/j.socscimed.2025.117720},
pmid = {39889380},
issn = {1873-5347},
abstract = {Policymakers and researchers have posited intrapartum care as a potential mediator of racial inequities in perinatal outcomes. However, few studies have measured patient-centered quality of intrapartum care or explored differences by race. To address this gap, we developed a survey supplement using cognitive interviewing and administered it to a probability-based race-stratified random sample of people who recently gave birth in Wisconsin in 2020, including oversamples of non-Hispanic Black and Indigenous birthing people. We estimate overall and race-specific prevalences of intrapartum care experiences and use survey-weighted mixed effects ordinal and logistic regression to estimate differences in intrapartum care experiences by race/ethnicity and hospital characteristics. We find significant racial differences in the population prevalence of negative experiences of intrapartum care providers, including disrespect, lack of responsiveness, inclusion in decision-making about care, and pressure to use epidural analgesia. In unadjusted models, both non-Hispanic Indigenous (American Indian/Alaska Native) and non-Hispanic Black respondents had higher odds (than non-Hispanic White birthing people) of reporting several negative intrapartum experiences, including feeling disrespected by providers and experiencing a lower level of care team responsiveness. In adjusted models, Indigenous respondents had significantly higher odds of reporting that intrapartum care providers withheld information, showed disrespect, and were less responsive. Giving birth at a low birth-volume hospital was associated with higher odds of reporting greater participation in decision-making. CONCLUSION: While all birthing people are entitled to respectful and person-centered care, in practice, Indigenous and Black birthing persons are more likely than their white counterparts to endure negative intrapartum experiences including disrespect and lack of responsiveness to their needs. Equitable implementation of person-centered care principles will require concerted efforts to institutionalize practices that preserve patient dignity and autonomy.},
}

@article {pmid39888239,
year = {2025},
author = {Giles, EC and González, VL and Carimán, P and Leiva, C and Suescún, AV and Lemer, S and Guillemin, ML and Ortiz-Barrientos, D and Saenz-Agudelo, P},
title = {Comparative Genomics Points to Ecological Drivers of Genomic Divergence Among Intertidal Limpets.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14075},
doi = {10.1111/1755-0998.14075},
pmid = {39888239},
issn = {1755-0998},
support = {2190878//BECA CONICYT-PCHA/Doctorado Nacional Chile/2019/ ; 1190710//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; },
abstract = {Comparative genomic studies of closely related taxa are important for our understanding of the causes of divergence on a changing Earth. This being said, the genomic resources available for marine intertidal molluscs are limited and currently, there are few publicly available high-quality annotated genomes for intertidal species and for molluscs in general. Here we report transcriptome assemblies for six species of Patellogastropoda and genome assemblies and annotations for three of these species (Scurria scurra, Scurria viridula and Scurria zebrina). Comparative analysis using these genomic resources suggest that and recently diverging lineages (10-20 Mya) have experienced similar amounts of contractions and expansions but across different gene families. Furthermore, differences among recently diverged species are reflected in variation in the amount of coding and noncoding material in genomes, such as amount of repetitive elements and lengths of transcripts and introns and exons. Additionally, functional ontologies of species-specific and duplicated genes together with demographic inference support the finding that recent divergence among members of the genus Scurria aligns with their unique ecological characteristics. Overall, the resources presented here will be valuable for future studies of adaptation in molluscs and in intertidal habitats as a whole.},
}

@article {pmid39854567,
year = {2025},
author = {Moody, NM and Williams, CM and Ramachandran, S and Fuxjager, MJ},
title = {Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012740},
doi = {10.1371/journal.pcbi.1012740},
pmid = {39854567},
issn = {1553-7358},
mesh = {Animals ; Female ; Male ; *Aggression/physiology ; *Territoriality ; Birds/physiology ; Computational Biology ; Social Behavior ; Behavior, Animal/physiology ; Sexual Behavior, Animal/physiology ; },
abstract = {Negotiating social dynamics among allies and enemies is a complex problem that often requires individuals to tailor their behavioral approach to a specific situation based on environmental and/or social factors. One way to make these contextual adjustments is by arranging behavioral output into intentional patterns. Yet, few studies explore how behavioral patterns vary across a wide range of contexts, or how allies might interlace their behavior to produce a coordinated response. Here, we investigate the possibility that resident female and male downy woodpeckers guard their breeding territories from conspecific intruders by deploying defensive behavior in context-specific patterns. To study whether this is the case, we use correlation networks to reveal how suites of agonistic behavior are interrelated. We find that residents do organize their defense into definable patterns, with female and male social mates deploying their behaviors non-randomly in a correlated fashion. We then employ spectral clustering analyses to further distill these responses into distinct behavioral motifs. Our results show that this population of woodpeckers adjusts the defensive motifs deployed according to threat context. When we combine this approach with behavioral transition analyses, our results reveal that pair coordination is a common feature of territory defense in this species. However, if simulated intruders are less threatening, residents are more likely to defend solo, where only one bird deploys defensive behaviors. Overall, our study supports the hypothesis that nonhuman animals can pattern their behavior in a strategic and coordinated manner, while demonstrating the power of systems approaches for analyzing multiagent behavioral dynamics.},
}

Animals
Female
Male
*Aggression/physiology
*Territoriality
Birds/physiology
Computational Biology
Social Behavior
Behavior, Animal/physiology
Sexual Behavior, Animal/physiology

@article {pmid38112302,
year = {2025},
author = {Marques, PH and Rodrigues, TCV and Santos, EH and Bleicher, L and Aburjaile, FF and Martins, FS and Oliveira, CJF and Azevedo, V and Tiwari, S and Soares, S},
title = {Design of a multi-epitope vaccine (vme-VAC/MST-1) against cholera and vibriosis based on reverse vaccinology and immunoinformatics approaches.},
journal = {Journal of biomolecular structure & dynamics},
volume = {43},
number = {4},
pages = {1788-1803},
doi = {10.1080/07391102.2023.2293256},
pmid = {38112302},
issn = {1538-0254},
mesh = {*Cholera/prevention & control/immunology ; *Computational Biology/methods ; Humans ; *Cholera Vaccines/immunology ; *Vaccinology/methods ; Epitopes, T-Lymphocyte/immunology/chemistry ; Epitopes/immunology/chemistry ; Epitopes, B-Lymphocyte/immunology/chemistry ; Vibrio Infections/prevention & control/immunology ; Molecular Docking Simulation ; Immunoinformatics ; },
abstract = {Vibriosis and cholera are serious diseases distributed worldwide and caused by six marine bacteria of the Vibrio genus. Thousands of deaths occur each year due to these illnesses, necessitating the development of new preventive measures. Presently, the existing cholera vaccine demonstrates an effectiveness of approximately 60%. Here we describe a new multi-epitope vaccine, 'vme-VAC/MST-1' based on vaccine targets identified by reverse vaccinology and epitopes predicted by immunoinformatics, two currently effective tools for predicting new vaccines for bacterial pathogens. The vaccine was designed to combat vibriosis and cholera by incorporating epitopes predicted for CTL, HTL, and B cells. These epitopes were identified from six vaccine targets revealed through subtractive genomics, combined with reverse vaccinology, and were further filtered using immunoinformatics approaches based on their predicted immunogenicity. To construct the vaccine, 28 epitopes (24 CTL/B and 4 HTL/B) were linked to the sequence of the cholera toxin B subunit adjuvant. In silico analyses indicate that the resulting immunogen is stable, soluble, non-toxic, and non-allergenic. Furthermore, it exhibits no homology to the host and demonstrates a strong capacity to elicit innate, B-cell, and T-cell immune responses. Our analysis suggests that it is likely to elicit immune reactions mediated through the TLR5 pathway, as evidenced by the molecular docking of the vaccine with the receptor, which revealed high affinity and a favorable reaction. Thus, vme-VAC/MST-1 is predicted to be a safe and effective solution against pathogenic Vibrio spp. However, further experimental analyses are required to measure the vaccine's effects In vivo.Communicated by Ramaswamy H. Sarma.},
}

*Cholera/prevention & control/immunology
*Computational Biology/methods
Humans
*Cholera Vaccines/immunology
*Vaccinology/methods
Epitopes, T-Lymphocyte/immunology/chemistry
Epitopes/immunology/chemistry
Epitopes, B-Lymphocyte/immunology/chemistry
Vibrio Infections/prevention & control/immunology
Molecular Docking Simulation
Immunoinformatics

@article {pmid39834325,
year = {2025},
author = {Chen, L and Xu, Z and He, Y and Zhang, X and Li, L and Zhu, R and Zhang, Z and Lin, H and Hong, G},
title = {Multiomics Analysis Reveals Key Targeted Metabolic Pathways Underlying the Hormesis and Detrimental Effects of Enrofloxacin on Rice Plants.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {4},
pages = {2678-2695},
doi = {10.1021/acs.jafc.4c09001},
pmid = {39834325},
issn = {1520-5118},
mesh = {*Oryza/metabolism/growth & development/drug effects/genetics/chemistry ; *Enrofloxacin/metabolism ; *Hormesis/drug effects ; *Metabolic Networks and Pathways/drug effects ; Anti-Bacterial Agents/pharmacology ; Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/drug effects ; Multiomics ; },
abstract = {Fluoroquinolone antibiotic enrofloxacin (ENR) is frequently detected in agricultural environments. The hormesis and detrimental effects of ENR on crops have been extensively observed. However, the molecular mechanisms underlying these crops' responses to ENR remain limited. Here, integrated physiological, transcriptomic, and metabolomic analysis revealed the key metabolic pathway responses underlying the ENR-induced effects on rice. The results showed that ENR mainly affected three metabolic pathways: 'biosynthesis of amino acids', "tryptophan metabolism", and 'phenylpropanoid/flavonoid biosynthesis'. A low level of ENR treatment promoted root elongation and enhanced the antioxidant capacity by increasing the phytohormone gibberellin A3 and the flavonol quercetin-3-O-neohesperidoside, respectively. However, the high dose of ENR significantly stimulated ROS production, inhibited photosynthesis, and ultimately impaired plant growth. In response to high ENR toxicity, plants accumulated more quercetin derivatives as antioxidants and produced defense-related substances, such as N-hydroxytryptamine, indole-3-acetonitrile, and jasmonic acid, to combat biotic stress. In conclusion, this study provides new insights into the molecular mechanism accounting for the ecological effects of antibiotic pollution in farmland.},
}

*Oryza/metabolism/growth & development/drug effects/genetics/chemistry
*Enrofloxacin/metabolism
*Hormesis/drug effects
*Metabolic Networks and Pathways/drug effects
Anti-Bacterial Agents/pharmacology
Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant/drug effects
Multiomics

@article {pmid39874571,
year = {2025},
author = {Sahandi Far, M and Fischer, JM and Senge, S and Rathmakers, R and Meissner, T and Schneble, D and Narava, M and Eickhoff, SB and Dukart, J},
title = {Cross-Platform Ecological Momentary Assessment App (JTrack-EMA+): Development and Usability Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e51689},
doi = {10.2196/51689},
pmid = {39874571},
issn = {1438-8871},
mesh = {Humans ; *Ecological Momentary Assessment ; *Mobile Applications ; Smartphone ; },
abstract = {BACKGROUND: Traditional in-clinic methods of collecting self-reported information are costly, time-consuming, subjective, and often limited in the quality and quantity of observation. However, smartphone-based ecological momentary assessments (EMAs) provide complementary information to in-clinic visits by collecting real-time, frequent, and longitudinal data that are ecologically valid. While these methods are promising, they are often prone to various technical obstacles. However, despite the potential of smartphone-based EMAs, they face technical obstacles that impact adaptability, availability, and interoperability across devices and operating systems. Deficiencies in these areas can contribute to selection bias by excluding participants with unsupported devices or limited digital literacy, increase development and maintenance costs, and extend deployment timelines. Moreover, these limitations not only impede the configurability of existing solutions but also hinder their adoption for addressing diverse clinical challenges.

OBJECTIVE: The primary aim of this research was to develop a cross-platform EMA app that ensures a uniform user experience and core features across various operating systems. Emphasis was placed on maximizing the integration and adaptability to various study designs, all while maintaining strict adherence to security and privacy protocols. JTrack-EMA+ was designed and implemented per the FAIR (findable, accessible, interpretable, and reusable) principles in both its architecture and data management layers, thereby reducing the burden of integration for clinicians and researchers.

METHODS: JTrack-EMA+ was built using the Flutter framework, enabling it to run seamlessly across different platforms. This platform comprises two main components. JDash (Research Centre Jülich, Institute of Neuroscience and Medicine, Brain and Behaviour [INM-7]) is an online management tool created using Python (Python Software Foundation) with the Django (Django Software Foundation) framework. This online dashboard offers comprehensive study management tools, including assessment design, user administration, data quality control, and a reminder casting center. The JTrack-EMA+ app supports a wide range of question types, allowing flexibility in assessment design. It also has configurable assessment logic and the ability to include supplementary materials for a richer user experience. It strongly commits to security and privacy and complies with the General Data Protection Regulations to safeguard user data and ensure confidentiality.

RESULTS: We investigated our platform in a pilot study with 480 days of follow-up to assess participants' compliance. The 6-month average compliance was 49.3%, significantly declining (P=.004) from 66.7% in the first month to 42% in the sixth month.

CONCLUSIONS: The JTrack-EMA+ platform prioritizes platform-independent architecture, providing an easy entry point for clinical researchers to deploy EMA in their respective clinical studies. Remote and home-based assessments of EMA using this platform can provide valuable insights into patients' daily lives, particularly in a population with limited mobility or inconsistent access to health care services.},
}

Humans
*Ecological Momentary Assessment
*Mobile Applications
Smartphone

@article {pmid39813804,
year = {2025},
author = {Ahmad, S and Peng, X and Ashraf, A and Yin, D and Chen, Z and Ahmed, R and Israr, M and Jia, H},
title = {Building resilient urban drainage systems by integrated flood risk index for evidence-based planning.},
journal = {Journal of environmental management},
volume = {374},
number = {},
pages = {124130},
doi = {10.1016/j.jenvman.2025.124130},
pmid = {39813804},
issn = {1095-8630},
mesh = {*Floods ; *Cities ; Geographic Information Systems ; Climate Change ; Risk Management/methods ; Urbanization ; Risk Assessment ; },
abstract = {Urban flooding poses a significant risk to cities worldwide, exacerbated by increasing urbanization and climate change. Effective flood risk management requires comprehensive assessments considering the complex interaction of social, economic, and environmental factors. This study developed an innovative Urban Flood Risk Index (FRI) to quantify and assess flood risk at the sub-catchment level, providing a tool for evidence-based planning and resilient infrastructure development. This study integrates Geographic Information System (GIS), Storm Water Management Model (SWMM), Analytic Hierarchy Process (AHP), and the Pressure-State-Response (PSR) framework. The FRI incorporates seven pressure and state indicators and three response indicators weighted by expert judgment. The FRI was calculated by combining the weighted sub-indices, classifying flood risk into five levels. Results showed that 51% of the study area experienced high pressure, with 26% facing very-high pressure. The state index indicated that 55% of the area falls under a moderate state, while 21% exhibits a high state. Importantly, the response index highlighted the effectiveness of Low Impact Development (LID) practices, with 20% of the area showing high to very-high response levels. The integrated FRI demonstrated an overall moderate flood risk level for maximum sub-catchments, emphasizing the positive impact of LID practices in mitigating flood risk despite existing pressures and system limitations. This evidence-based assessment provides a valuable tool for sub-catchment level flood risk assessment. It empowers decision-makers to prioritize investments, target interventions, and develop adaptive strategies to enhance urban resilience in a changing climate.},
}

*Floods
*Cities
Geographic Information Systems
Climate Change
Risk Management/methods
Urbanization
Risk Assessment

@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {7},
number = {1},
pages = {16-34},
pmid = {39809974},
issn = {2522-5812},
mesh = {Humans ; China/epidemiology ; *Diabetes Mellitus/epidemiology ; Risk Factors ; Prevalence ; Metabolomics ; Multiomics ; },
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}

Humans
China/epidemiology
*Diabetes Mellitus/epidemiology
Risk Factors
Prevalence
Metabolomics
Multiomics

@article {pmid39648557,
year = {2025},
author = {Huang, Y and Wang, T and Li, Y and Wang, Z and Cai, X and Chen, J and Li, R and Li, X},
title = {In Vitro-to-In Vivo Extrapolation on Lung Toxicity Induced by Metal Oxide Nanoparticles via Data-Mining.},
journal = {Environmental science & technology},
volume = {59},
number = {3},
pages = {1673-1682},
doi = {10.1021/acs.est.4c06186},
pmid = {39648557},
issn = {1520-5851},
mesh = {*Lung/drug effects/pathology ; Animals ; *Metal Nanoparticles/toxicity ; Mice ; *Oxides/toxicity ; Data Mining ; Humans ; },
abstract = {While in silico analyses are commonly employed for chemical risk assessments, predicting chronic lung toxicity induced by engineered nanoparticles (ENMs) in vivo still faces many challenges due to complex interactions at multiple nanobio interfaces. In this study, we developed a rigorous method to compile published evidence on the in vivo lung toxicity of metal oxide nanoparticles (MeONPs) and revealed previously overlooked in vitro-to-in vivo extrapolation (IVIVE) relationships. A comprehensive multidimensional data set containing 1102 in vivo data points, 75 pulmonary toxicological biomarkers, and 20 features (covering in vitro effects, physicochemical properties, and exposure conditions) was constructed. An IVIVE approach that related effects at the cellular level to in vivo lung toxicity in rodent model was established with prediction accuracy reaching 89 and 80% in training and test sets. Experimental validation was conducted by testing chronic lung fibrosis of 8 new MeONPs in 32 independent mice, with prediction accuracy reaching 88%. The IVIVE model indicated that the proinflammatory cytokine IL-1β in THP-1 cells could serve as an in vitro marker to predict lung toxicity. The IVIVE model showed great promise for minimizing unnecessary animal tests and understanding toxicological mechanisms.},
}

*Lung/drug effects/pathology
Animals
*Metal Nanoparticles/toxicity
Mice
*Oxides/toxicity
Data Mining
Humans

@article {pmid39870942,
year = {2025},
author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H},
title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39870942},
issn = {1708-0428},
abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.

METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10 GB. Evaluations before (0 M) and 6 months (6 M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16 s rRNA next-generation sequencing approach. Statistical significance was set to a p value < 0.05 with an FDR < 0.1.

RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6 M showed near significant differences (p = 0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.

CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.},
}

@article {pmid39870652,
year = {2025},
author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y},
title = {A quantitative prediction method utilizing whole omics data for biosensing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1928},
pmid = {39870652},
issn = {2045-2322},
support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; },
mesh = {*Biosensing Techniques/methods ; *Biomarkers ; Transcriptome ; Humans ; Metabolomics/methods ; Gene Regulatory Networks ; Genomics/methods ; Computational Biology/methods ; Metabolome ; Microbiota/genetics ; Gene Expression Profiling/methods ; },
abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.},
}

*Biosensing Techniques/methods
*Biomarkers
Transcriptome
Humans
Metabolomics/methods
Gene Regulatory Networks
Genomics/methods
Computational Biology/methods
Metabolome
Microbiota/genetics
Gene Expression Profiling/methods

@article {pmid39871100,
year = {2025},
author = {Terauds, A and Lee, JR and Wauchope, HS and Raymond, B and Bergstrom, DM and Convey, P and Mason, C and Patterson, CR and Robinson, SA and Van de Putte, A and Watts, D and Chown, SL},
title = {The biodiversity of ice-free Antarctica database.},
journal = {Ecology},
volume = {106},
number = {1},
pages = {e70000},
doi = {10.1002/ecy.70000},
pmid = {39871100},
issn = {1939-9170},
support = {n°FR/36/AN1/AntaBIS(EU-LifeWatch)//Belgian Science Policy Office/ ; n°RT/23/ADVANCE//Belgian Science Policy Office/ ; //Royal Commission for the Exhibition of 1851 Research Fellowship/ ; SRIEAS-SR200100005//Australian Research Council/ ; //Securing Antarctica's Environmental Future/ ; AAS 4296//Australian Antarctic Division/ ; AAS 4297//Australian Antarctic Division/ ; },
abstract = {Antarctica is one of Earth's most untouched, inhospitable, and poorly known regions. Although knowledge of its biodiversity has increased over recent decades, a diverse, wide-ranging, and spatially explicit compilation of the biodiversity that inhabits Antarctica's permanently ice-free areas is unavailable. This absence hinders both Antarctic biodiversity research and the integration of Antarctica in global biodiversity-related studies. Fundamental and applied research on biodiversity patterns, ecological structure and function, and options for conservation are reliant on spatially resolved, taxonomically consistent observations. Such information is especially important for modern, data-driven biodiversity science, in both Antarctica and globally, and forms the backbone of biodiversity informatics, reflected, for example, in the Darwin Core Standard used by the Global Biodiversity Information Facility. Biodiversity data are also essential to fulfill the conservation requirements for Antarctica, as set out in the Protocol on Environmental Protection to the Antarctic Treaty and inform the design of systematic surveys to address biodiversity and ecological knowledge gaps, for both specific taxa and ecosystems. Such surveys are key requirements for understanding and mitigating the impacts of environmental change on the region's biodiversity. Here, we address these requirements through the public release of The Biodiversity of Ice-free Antarctica Database. In 2008, we extracted a subset of biodiversity records only from terrestrial ice-free areas from the Scientific Committee on Antarctic Research (SCAR) Antarctic Biodiversity Database. We have subsequently added thousands of records from a range of sources: checking, and where necessary (and possible), correcting the spatial location, clarifying, cross-referencing, and harmonizing taxonomy with globally recognized sources, and documenting the original source of records. The Biodiversity of Ice-free Antarctica Database spans the early 1800s to 2019 (with most records collected after 1950) and represents the most comprehensive consolidation of Antarctic ice-free biodiversity occurrence data yet compiled into a single database. The Biodiversity of Ice-free Antarctica Database contains 35,654 records of 1890 species in over 800 genera across six kingdoms and spans all Antarctic Conservation Biogeographic Regions. These data are released under a CC BY Attribution License (http://creativecommons.org/licenses/by/4.0/).},
}

@article {pmid39870651,
year = {2025},
author = {Ridgway, J and Wesner, J},
title = {A global dataset of freshwater fish trophic interactions.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {160},
pmid = {39870651},
issn = {2052-4463},
mesh = {Animals ; *Fishes ; *Fresh Water ; Food Chain ; Diet/veterinary ; Predatory Behavior ; Databases, Factual ; },
abstract = {Freshwater management and research frequently rely on trophic data to manage freshwater fishes, yet it is difficult to perform a simple search of dietary information for any one species. FishBase represents the largest effort to organize freshwater dietary data into a singular, navigable dataset. Nonetheless, FishBase excludes a large portion of the ecological literature because it was developed before the creation of most modern scientific search engines. Our project, TroPhish, builds upon FishBase by digitizing over 100 years of data from the fish predation literature. Data from 1,106 published papers, theses, dissertations, and government reports were filtered, scanned in through third-party software (Able2Extract), reorganized, and consolidated with FishBase to form a unified dataset. This dataset contains 54,750 observations of data on 4,571 unique dietary samples, representing 9% (982) of all freshwater fish species and 43% (111) of all freshwater fish families. Fish species and family representation varied by continent, ranging from 3-32% and 34-75%, respectively. Users are encouraged to submit errors or additional data through GitHub's fork and pull model.},
}

Animals
*Fishes
*Fresh Water
Food Chain
Diet/veterinary
Predatory Behavior
Databases, Factual

@article {pmid39869900,
year = {2025},
author = {Yeom, JW and Kim, H and Pack, SP and Lee, HJ and Cheong, T and Cho, CH},
title = {Exploring the Psychological and Physiological Insights Through Digital Phenotyping by Analyzing the Discrepancies Between Subjective Insomnia Severity and Activity-Based Objective Sleep Measures: Observational Cohort Study.},
journal = {JMIR mental health},
volume = {12},
number = {},
pages = {e67478},
doi = {10.2196/67478},
pmid = {39869900},
issn = {2368-7959},
mesh = {Humans ; Middle Aged ; Male ; *Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis ; Female ; Adult ; *Severity of Illness Index ; Aged ; Cohort Studies ; *Wearable Electronic Devices ; Young Adult ; Ecological Momentary Assessment ; Sleep/physiology ; Exercise/psychology/physiology ; Self Report ; },
abstract = {BACKGROUND: Insomnia is a prevalent sleep disorder affecting millions worldwide, with significant impacts on daily functioning and quality of life. While traditionally assessed through subjective measures such as the Insomnia Severity Index (ISI), the advent of wearable technology has enabled continuous, objective sleep monitoring in natural environments. However, the relationship between subjective insomnia severity and objective sleep parameters remains unclear.

OBJECTIVE: This study aims to (1) explore the relationship between subjective insomnia severity, as measured by ISI scores, and activity-based objective sleep parameters obtained through wearable devices; (2) determine whether subjective perceptions of insomnia align with objective measures of sleep; and (3) identify key psychological and physiological factors contributing to the severity of subjective insomnia complaints.

METHODS: A total of 250 participants, including both individuals with and without insomnia aged 19-70 years, were recruited from March 2023 to November 2023. Participants were grouped based on ISI scores: no insomnia, mild, moderate, and severe insomnia. Data collection involved subjective assessments through self-reported questionnaires and objective measurements using wearable devices (Fitbit Inspire 3) that monitored sleep parameters, physical activity, and heart rate. The participants also used a smartphone app for ecological momentary assessment, recording daily alcohol consumption, caffeine intake, exercise, and stress. Statistical analyses were used to compare groups on subjective and objective measures.

RESULTS: Results indicated no significant differences in general sleep structure (eg, total sleep time, rapid eye movement sleep time, and light sleep time) among the insomnia groups (mild, moderate, and severe) as classified by ISI scores (all P>.05). Interestingly, the no insomnia group had longer total awake times and lower sleep quality compared with the insomnia groups. Among the insomnia groups, no significant differences were observed regarding sleep structure (all P>.05), suggesting similar sleep patterns regardless of subjective insomnia severity. There were significant differences among the insomnia groups in stress levels, dysfunctional beliefs about sleep, and symptoms of restless leg syndrome (all P≤.001), with higher severity associated with higher scores in these factors. Contrary to expectations, no significant differences were observed in caffeine intake (P=.42) and alcohol consumption (P=.07) between the groups.

CONCLUSIONS: The findings demonstrate a discrepancy between subjective perceptions of insomnia severity and activity-based objective sleep parameters, suggesting that factors beyond sleep duration and quality may contribute to subjective sleep complaints. Psychological factors, such as stress, dysfunctional sleep beliefs, and symptoms of restless legs syndrome, appear to play significant roles in the perception of insomnia severity. These results highlight the importance of considering both subjective and objective assessments in the evaluation and treatment of insomnia and suggest potential avenues for personalized treatment strategies that address both psychological and physiological aspects of sleep disturbances.

TRIAL REGISTRATION: Clinical Research Information Service KCT0009175; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26133.},
}

Humans
Middle Aged
Male
*Sleep Initiation and Maintenance Disorders/physiopathology/psychology/diagnosis
Female
Adult
*Severity of Illness Index
Aged
Cohort Studies
*Wearable Electronic Devices
Young Adult
Ecological Momentary Assessment
Sleep/physiology
Exercise/psychology/physiology
Self Report

@article {pmid39868965,
year = {2025},
author = {Grikscheit, K and Berger, A and Rabenau, H and Kohmer, N and Appel, KS and Scherer, M and Bals, R and Blaschke, S and Hamprecht, A and Hopff, SM and Krefting, D and Meybohm, P and Nürnberger, C and Heuschmann, P and Pley, C and Nunes de Miranda, SM and Dahl, E and Jensen, B and Illig, T and Anton, G and Vehreschild, JJ and Ciesek, S},
title = {Occurrence and clinical correlates of SARS-CoV-2 viremia in two German patient cohorts.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2459137},
doi = {10.1080/22221751.2025.2459137},
pmid = {39868965},
issn = {2222-1751},
abstract = {Viremia defined as detectable SARS-CoV-2 RNA in the blood is a potential marker of disease severity and prognosis in COVID-19 patients. Here, we determined the frequency of viremia in serum of two independent COVID-19 patient cohorts within the German National Pandemic Cohort Network (German: Nationales Pandemie Kohorten Netzwerk, NAPKON) with diagnostic RT-PCR against SARS-CoV-2. A cross-sectional cohort with 1,122 COVID-19 patients (German: Sektorenuebergreifende Platform, SUEP) and 299 patients recruited in a high-resolution platform with patients at high risk to develop severe courses (German: Hochaufloesende Plattform, HAP) were tested for viremia. Our study also involved a comprehensive analysis and association of serological, diagnostic and clinical parameters of the NAPKON medical dataset. Prevalence of viremia at the recruitment visit was 12,8% (SUEP) and 13% (HAP) respectively. Serological analysis revealed that viremic patients had lower levels of SARS-CoV-2 specific antibodies as well as lower neutralizing antibodies compared to aviremic patients. Viremia was associated with severity (<0.0001 SUEP; 0.002 HAP) and mortality of COVID-19 (both cohorts <0.0001) compared to aviremic patients. While rare, viremia was also detected in patients with mild disease (0.7%). In patients of the SUEP cohort with acute kidney disease (p = 0.0099) and hematooncological conditions (p = 0.0091), viremia was detected more frequently. Compared to the aviremic group, treatment with immunomodulating drugs as well as elevated levels of inflammatory markers in the blood was more frequent in the viremic group. In conclusion, our analysis revealed that detectable viremia correlates with hyperinflammatory conditions and higher risk for severe COVID-19 disease.},
}

@article {pmid39830079,
year = {2024},
author = {Couch, J and Arnaout, R and Arnaout, R},
title = {Beyond Size and Class Balance: Alpha as a New Dataset Quality Metric for Deep Learning.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39830079},
issn = {2331-8422},
support = {R01 AI148747/AI/NIAID NIH HHS/United States ; R01 HL150394/HL/NHLBI NIH HHS/United States ; },
abstract = {In deep learning, achieving high performance on image classification tasks requires diverse training sets. However, the current best practice-maximizing dataset size and class balance-does not guarantee dataset diversity. We hypothesized that, for a given model architecture, model performance can be improved by maximizing diversity more directly. To test this hypothesis, we introduce a comprehensive framework of diversity measures from ecology that generalizes familiar quantities like Shannon entropy by accounting for similarities among images. (Size and class balance emerge as special cases.) Analyzing thousands of subsets from seven medical datasets showed that the best correlates of performance were not size or class balance but A -"big alpha"-a set of generalized entropy measures interpreted as the effective number of image-class pairs in the dataset, after accounting for image similarities. One of these, A 0 , explained 67% of the variance in balanced accuracy, vs. 54% for class balance and just 39% for size. The best pair of measures was size-plus- A 1 (79%), which outperformed size-plus-class-balance (74%). Subsets with the largest A 0 performed up to 16% better than those with the largest size (median improvement, 8%). We propose maximizing A as a way to improve deep learning performance in medical imaging.},
}

@article {pmid39866757,
year = {2023},
author = {Gudelj Rakić, J and Maksimović, M and Vlajinac, H and Janković, J and Vukašinović, D and Marinković, J},
title = {TRENDS IN OVERWEIGHT AND OBESITY AMONG SERBIAN ADULT POPULATION 2000-2013.},
journal = {Acta clinica Croatica},
volume = {62},
number = {4},
pages = {605-614},
pmid = {39866757},
issn = {1333-9451},
mesh = {Humans ; Male ; Serbia/epidemiology ; Female ; Adult ; *Obesity/epidemiology ; *Overweight/epidemiology ; Prevalence ; Middle Aged ; *Body Mass Index ; Cross-Sectional Studies ; Health Surveys ; Young Adult ; Aged ; },
abstract = {The aim of the study was to determine changes in body mass index (BMI) and in the prevalence of overweight and obesity in Serbian adult population. Data for this study were obtained from three National Health Interview Surveys, carried out as cross-sectional, nationally representative surveys in 2000, 2006 and 2013. The values of p for trends of sociodemographic and health related behavioral characteristics, of BMI distribution, and of overweight and obesity prevalence were determined by univariate and multivariate linear and logistic regression analyses, with year of survey as a continuous variable. The mean values of BMI and standard deviations in surveys were 26.09±3.92, 26.28±4.02 and 26.87±4.33 in men, and 25.91±5.25, 25.77±5.22 and 26.35±5.58 in women, respectively (trend p<0.001 both). The prevalence of obesity was 14.3%, 16.5% and 21.4% in men, and 20.0%, 19.7% and 23.3% in women, respectively (trend p<0.001 both). The prevalence of overweight did not change significantly during the observed period. In conclusion, the prevalence of obesity showed an increasing trend in both men and women, demanding targeted public health interventions.},
}

Humans
Male
Serbia/epidemiology
Female
Adult
*Obesity/epidemiology
*Overweight/epidemiology
Prevalence
Middle Aged
*Body Mass Index
Cross-Sectional Studies
Health Surveys
Young Adult
Aged

@article {pmid39865039,
year = {2024},
author = {Alekseeva, AO and Zolotovskaia, MA and Sorokin, MI and Suntsova, MV and Zakharova, GS and Pugacheva, PA and Tinkov, AA and Korobeinikova, TV and Sekacheva, MI and Poddubskaya, EV and Skalny, AV and Kushlinskii, NE and Buzdin, AA},
title = {The First Multiomics Association Study of Trace Element and Mineral Concentration and RNA Sequencing Profiles in Human Cancers.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {12},
pages = {2274-2286},
doi = {10.1134/S0006297924120150},
pmid = {39865039},
issn = {1608-3040},
mesh = {Humans ; *Trace Elements/metabolism/analysis ; Minerals/metabolism ; Sequence Analysis, RNA ; Neoplasms/genetics/metabolism ; Male ; Colorectal Neoplasms/genetics/metabolism ; Female ; Gene Expression Profiling ; Multiomics ; },
abstract = {Integration of various types of omics data is an important trend in contemporary molecular oncology. In this regard, high-throughput analysis of trace and essential elements in cancer biosamples is an emerging field that has not yet been sufficiently addressed. For the first time, we simultaneously obtained gene expression profiles (RNA sequencing) and essential and trace element profiles (inductively coupled plasma mass spectrometry) for a set of human cancer samples. The biosamples were formalin-fixed, paraffin-embedded primary tumor tissue blocks: 67 for colorectal cancer patients and 18 for other solid cancer types (16 types). Mass spectrometry profiles were obtained for 45 chemical elements: Ag, Al, As, Au, B, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Fe, Ga, Ge, Hg, I, K, La, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Pd, Pt, Rb, Sb, Sc, Se, Si, Sn, Sr, Te, Ti, Tl, Zn, U, V, W, and Zr. The expression levels were profiled for 36,596 known human genes, and the activation levels were assessed for 10,520 human intracellular molecular pathways. For the concentrations of essential elements Ca, Cu, Fe, K, Mg, Na, P, and Zn we detected statistically significant correlations on both gene expression and pathway activation levels for both colorectal cancer samples and at the pan-cancer level. In total, 222/137, 122/220, 1/0, 239/186, 71/44, 1/0, 354/294, 69/82 gene/pathway biomarkers were detected for Ca, Cu, Fe, K, Mg, Na, P, and Zn, respectively. We believe that this first-in-class database provided here will be valuable for multiomics cancer research.},
}

Humans
*Trace Elements/metabolism/analysis
Minerals/metabolism
Sequence Analysis, RNA
Neoplasms/genetics/metabolism
Male
Colorectal Neoplasms/genetics/metabolism
Female
Gene Expression Profiling
Multiomics

@article {pmid39860723,
year = {2025},
author = {Dewmini, H and Meedeniya, D and Perera, C},
title = {Elephant Sound Classification Using Deep Learning Optimization.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {2},
pages = {},
doi = {10.3390/s25020352},
pmid = {39860723},
issn = {1424-8220},
mesh = {*Elephants/physiology ; *Deep Learning ; Animals ; *Vocalization, Animal/physiology ; *Bayes Theorem ; Sound Spectrography/methods ; Sound ; Algorithms ; },
abstract = {Elephant sound identification is crucial in wildlife conservation and ecological research. The identification of elephant vocalizations provides insights into the behavior, social dynamics, and emotional expressions, leading to elephant conservation. This study addresses elephant sound classification utilizing raw audio processing. Our focus lies on exploring lightweight models suitable for deployment on resource-costrained edge devices, including MobileNet, YAMNET, and RawNet, alongside introducing a novel model termed ElephantCallerNet. Notably, our investigation reveals that the proposed ElephantCallerNet achieves an impressive accuracy of 89% in classifying raw audio directly without converting it to spectrograms. Leveraging Bayesian optimization techniques, we fine-tuned crucial parameters such as learning rate, dropout, and kernel size, thereby enhancing the model's performance. Moreover, we scrutinized the efficacy of spectrogram-based training, a prevalent approach in animal sound classification. Through comparative analysis, the raw audio processing outperforms spectrogram-based methods. In contrast to other models in the literature that primarily focus on a single caller type or binary classification that identifies whether a sound is an elephant voice or not, our solution is designed to classify three distinct caller-types namely roar, rumble, and trumpet.},
}

*Elephants/physiology
*Deep Learning
Animals
*Vocalization, Animal/physiology
*Bayes Theorem
Sound Spectrography/methods
Sound
Algorithms

@article {pmid39856257,
year = {2025},
author = {Gulakhmadov, A and Chen, X and Gulahmadov, N and Rizwan, M and Gulakhmadov, M and Nadeem, MU and Rakhimova, M and Liu, T},
title = {Modeling of historical and future changes in temperature and precipitation in the Panj River Basin in Central Asia under the CMIP5 RCP and CMIP6 SSP scenarios.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {3037},
pmid = {39856257},
issn = {2045-2322},
support = {42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 42150410393//Research Fund for International Scientists of the National Natural Science Foundation of China/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 2023000137//Tianshan Talent Training Program of Xinjiang Uygur Autonomous region/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; 42230708/42361144887//National Natural Science Foundation of China/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; GJTD-2020-14//K.C. Wong Education Foundation/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; HZXM20225001MI//Joint CAS-MPG Research Project/ ; },
abstract = {This study examines the complexities of climate modeling, specifically in the Panj River Basin (PRB) in Central Asia, to evaluate the transition from CMIP5 to CMIP6 models. The research aimed to identify differences in historical simulations and future predictions of rainfall and temperature, examining the accuracy of eight General Circulation Models (GCMs) used in both CMIP5 (RCP4.5 and 8.5) and CMIP6 (SSP2-4.5 and 5-8.5). The evaluation metrics demonstrated that the GCMs have a high level of accuracy in reproducing maximum temperature (Tmax) with a correlation coefficient of 0.96. The models also performed well in replicating minimum temperature (Tmin) with a correlation coefficient of 0.94. This suggests that the models have improved modeling capabilities in both CMIPs. The performance of Max Plank Institute (MPI) across all variables in CMIP6 models was exceptional. Within the CMIP5 domain, Geophysical Fluid Dynamics (GFDL) demonstrated outstanding skill in reproducing maximum temperature (Tmax) and precipitation (KGE 0.58 and 0.34, respectively), while (Institute for Numerical Mathematics) INMCM excelled in replicating minimum temperature (Tmin) (KGE 0.28). The uncertainty analysis revealed a significant improvement in the CMIP6 precipitation bias bands, resulting in a more precise depiction of diverse climate zones compared to CMIP5. Both CMIPs consistently tended to underestimate Tmax in the Csa zone and overestimate it in the Bwk zone throughout all months. Nevertheless, the CMIP6 models demonstrated a significant decrease in uncertainty, especially in ensemble simulations, suggesting improvements in forecasting PRB climate dynamics. The projections revealed a complex story, as the CMIP6 models predict a relatively small increase in temperature and a simultaneous drop in precipitation. This indicates a trend towards more uniform temperature patterns across different areas. Nevertheless, the precipitation forecasts exhibited increased variability, highlighting the intricate interaction of climate dynamics in the PRB area under the impact of global warming scenarios. Hydrological components in global climate models can be further improved and developed with the theoretical reference provided by this study.},
}

@article {pmid39854555,
year = {2025},
author = {Zhou, J and Johnson, VC and Shi, J and Tan, ML and Zhang, F},
title = {Multi-scenario land use change simulation and spatial-temporal evolution of carbon storage in the Yangtze River Delta region based on the PLUS-InVEST model.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316255},
doi = {10.1371/journal.pone.0316255},
pmid = {39854555},
issn = {1932-6203},
mesh = {China ; *Rivers ; *Conservation of Natural Resources/methods ; *Carbon/metabolism/analysis ; Models, Theoretical ; Carbon Sequestration ; Ecosystem ; Spatio-Temporal Analysis ; Computer Simulation ; Humans ; Agriculture/methods ; },
abstract = {Influenced by urban expansion, population growth, and various socio-economic activities, land use in the Yangtze River Delta (YRD) area has undergone prominent changes. Modifications in land use have resulted in adjustments to ecological structures, leading to subsequent fluctuations in carbon storage. This study focuses on YRD region and analyzes the characteristics of land use changes in the area using land use data from 2000 to 2020, with a 10-year interval. Utilizing InVEST Model's Carbon Storage module in combination with PLUS model (patch-generating land use simulation), we simulated and projected future land use patterns and carbon storage across YRD region under five scenarios including natural development (ND), urban development (UD), ecological protection (EP), cropland protection (CP), and balanced development (BD). Upon comparing carbon storage levels predicted for 2030 under the five scenarios with those in 2020, carbon stocks decrease in the initial four scenarios and then increase in the fifth scenario. In the initial four declining scenarios, CP scenario had the least reduction in carbon storage, followed by EP scenario. The implementation of policies aimed at safeguarding cropland and preserving ecological integrity can efficaciously curtail the expansion of developed land into woodland and cropland, enhance the structure of land use, and mitigate the loss of carbon storage.},
}

China
*Rivers
*Conservation of Natural Resources/methods
*Carbon/metabolism/analysis
Models, Theoretical
Carbon Sequestration
Ecosystem
Spatio-Temporal Analysis
Computer Simulation
Humans
Agriculture/methods

@article {pmid39854538,
year = {2025},
author = {Katchali, M and Richard, E and Tonnang, HEZ and Tanga, CM and Beesigamukama, D and Senagi, K},
title = {Mathematical and computational modeling for organic and insect frass fertilizer production: A systematic review.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0292418},
doi = {10.1371/journal.pone.0292418},
pmid = {39854538},
issn = {1932-6203},
mesh = {*Fertilizers/analysis ; Animals ; *Insecta ; Models, Theoretical ; Agriculture/methods ; Computer Simulation ; },
abstract = {Organic fertilizers have been identified as a sustainable agricultural practice that can enhance productivity and reduce environmental impact. Recently, the European Union defined and accepted insect frass as an innovative and emerging organic fertilizer. In the wider domain of organic fertilizers, mathematical and computational models have been developed to optimize their production and application conditions. However, with the advancement in policies and regulations, modelling has shifted towards efficiencies in the deployment of these technologies. Therefore, this paper reviews and critically analyzes the recent developments in the mathematical and computation modeling that have promoted various organic fertilizer products including insect frass. We reviewed a total of 35 studies and discussed the methodologies, benefits, and challenges associated with the use of these models. The results show that mathematical and computational modeling can improve the efficiency and effectiveness of organic fertilizer production, leading to improved agricultural productivity and reduced environmental impact. Mathematical models such as simulation, regression, dynamics, and kinetics have been applied while computational data driven machine learning models such as random forest, support vector machines, gradient boosting, and artificial neural networks have also been applied as well. These models have been used in quantifying nutrients concentration/release, effects of nutrients in agro-production, and fertilizer treatment. This paper also discusses prospects for the use of these models, including the development of more comprehensive and accurate models and integration with emerging technologies such as Internet of Things.},
}

*Fertilizers/analysis
Animals
*Insecta
Models, Theoretical
Agriculture/methods
Computer Simulation

@article {pmid39853577,
year = {2025},
author = {Pierrat, ZA and Magney, TS and Richardson, WP and Runkle, BRK and Diehl, JL and Yang, X and Woodgate, W and Smith, WK and Johnston, MR and Ginting, YRS and Koren, G and Albert, LP and Kibler, CL and Morgan, BE and Barnes, M and Uscanga, A and Devine, C and Javadian, M and Meza, K and Julitta, T and Tagliabue, G and Dannenberg, MP and Antala, M and Wong, CYS and Santos, ALD and Hufkens, K and Marrs, JK and Stovall, AEL and Liu, Y and Fisher, JB and Gamon, JA and Cawse-Nicholson, K},
title = {Proximal remote sensing: an essential tool for bridging the gap between high-resolution ecosystem monitoring and global ecology.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.20405},
pmid = {39853577},
issn = {1469-8137},
support = {//National Research Council Postdoctoral Research Associateship Program/ ; 2020/37/B/ST10/01213//National Science Centre of Poland/ ; //TVL E-13 work contract at the Climate Monitoring Group of the University of Bonn/ ; //The LEMONTREE project by E. Schmidt and W. Schmidt/ ; 1926090//National Science Foundation/ ; 2044818//National Science Foundation/ ; 2131853//National Science Foundation/ ; IOS-2005574 OPP-2023205//National Science Foundation/ ; 80NSSC20K1805/NASA/NASA/United States ; 80NSSC21K1002/NASA/NASA/United States ; 80NSSC21K1639/NASA/NASA/United States ; 80NSSC21K1707/NASA/NASA/United States ; 80NSSC23K0109/NASA/NASA/United States ; 80NSSC23K0309/NASA/NASA/United States ; 80NSSC24K0135/NASA/NASA/United States ; NNH20ZDA001N-BIODIV/NASA/NASA/United States ; DE190101182//Australian Research Council/ ; },
abstract = {A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or 'proximal' remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability and metadata for proximal remote sensing: spectral reflectance, solar-induced fluorescence, thermal infrared radiation, microwave backscatter, and LiDAR. Our paper outlines the steps necessary for making these data streams more widespread, accessible, interoperable, and information-rich, enabling us to address key ecological questions unanswerable from space-based observations alone and, ultimately, to demonstrate the feasibility of these technologies to address critical questions in local and global ecology.},
}

@article {pmid39843543,
year = {2025},
author = {Gioiosa, S and Gasparini, S and Presutti, C and Rinaldi, A and Castrignanò, T and Mannironi, C},
title = {Integrated gene expression and alternative splicing analysis in human and mouse models of Rett syndrome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2778},
pmid = {39843543},
issn = {2045-2322},
support = {GJC22071//Cariplo Telethon Alliance/ ; },
mesh = {*Rett Syndrome/genetics ; Humans ; Animals ; *Alternative Splicing ; Mice ; *Disease Models, Animal ; *Methyl-CpG-Binding Protein 2/genetics/metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Computational Biology/methods ; Mutation ; },
abstract = {Mutations of the MECP2 gene lead to Rett syndrome (RTT), a rare developmental disease causing severe intellectual and physical disability. How the loss or defective function of MeCP2 mediates RTT is still poorly understood. MeCP2 is a global gene expression regulator, acting at transcriptional and post-transcriptional levels. Little attention has been given so far to the contribution of alternative splicing (AS) dysregulation to RTT pathophysiology. To perform a comparative analysis of publicly available RNA sequencing (RNA-seq) studies and generate novel data resources for AS, we explored 100 human datasets and 130 mouse datasets from Mecp2-mutant models, processing data for gene expression and alternative splicing. Our comparative analysis across studies indicates common species-specific differentially expressed genes (DEGs) and differentially alternatively spliced (DAS) genes. Human and mouse dysregulated genes are involved in two main functional categories: cell-extracellular matrix adhesion regulation and synaptic functions, the first category more significantly enriched in human datasets. Our extensive bioinformatics study indicates, for the first time, a significant dysregulation of AS in human RTT datasets, suggesting the crucial contribution of altered RNA processing to the pathophysiology of RTT.},
}

*Rett Syndrome/genetics
Humans
Animals
*Alternative Splicing
Mice
*Disease Models, Animal
*Methyl-CpG-Binding Protein 2/genetics/metabolism
Gene Expression Profiling
Gene Expression Regulation
Computational Biology/methods
Mutation

@article {pmid39841777,
year = {2025},
author = {Cardoso, ADRO and Ferreira, ACG and Rabahi, MF},
title = {Asthma-related deaths in Brazil: data from an ecological study.},
journal = {Jornal brasileiro de pneumologia : publicacao oficial da Sociedade Brasileira de Pneumologia e Tisilogia},
volume = {50},
number = {6},
pages = {e20240296},
doi = {10.36416/1806-3756/e20240296},
pmid = {39841777},
issn = {1806-3756},
mesh = {Humans ; Brazil/epidemiology ; *Asthma/mortality/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Hospitalization/statistics & numerical data ; Young Adult ; Adolescent ; Child ; Sex Distribution ; Age Distribution ; Child, Preschool ; Aged ; Infant ; Sex Factors ; Age Factors ; Cause of Death ; Time Factors ; },
abstract = {OBJECTIVE: The aim of this study was to present epidemiological data on hospitalizations and deaths related to asthma in Brazil over the past 11 years.

METHODS: An ecological study was conducted on asthma-related hospitalizations and mortality in Brazil from 2013 to 2023, using data extracted from the Department of Informatics of the Brazilian Unified Health System and the Mortality Information System.

RESULTS: Asthma-related deaths showed an increasing trend during the analyzed period. A surge in deaths was observed in 2022 compared to 2014 (difference between means = 56.08 ± 19.7; 95% CI = 15.2-96.9). The mean number of deaths was higher among females, with their rate remaining stable, while the rate for males increased. Individuals aged >60 years accounted for approximately 65% of all asthma-related deaths from 2013 to 2023, with a strong direct correlation observed between age and the number of deaths, regardless of sex. During the same period, the total number of asthma-related hospitalizations in Brazil showed a declining trend, decreasing from 134,322 in 2013 to 87,707 in 2023.

CONCLUSION: Over the past 11 years, asthma-related deaths have increased in Brazil, with the majority occurring among females. Older individuals accounted for most asthma-related deaths, and a positive correlation was observed between age and the number of deaths.},
}

Humans
Brazil/epidemiology
*Asthma/mortality/epidemiology
Male
Female
Middle Aged
Adult
*Hospitalization/statistics & numerical data
Young Adult
Adolescent
Child
Sex Distribution
Age Distribution
Child, Preschool
Aged
Infant
Sex Factors
Age Factors
Cause of Death
Time Factors

@article {pmid39840283,
year = {2024},
author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S},
title = {Recent advances in deep learning and language models for studying the microbiome.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1494474},
pmid = {39840283},
issn = {1664-8021},
abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.},
}

@article {pmid39838963,
year = {2024},
author = {Guan, J and Ji, Y and Peng, C and Zou, W and Tang, X and Shang, J and Sun, Y},
title = {GOPhage: protein function annotation for bacteriophages by integrating the genomic context.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf014},
pmid = {39838963},
issn = {1477-4054},
support = {11209823//City University of Hong Kong/ ; },
mesh = {*Bacteriophages/genetics ; *Genome, Viral ; *Molecular Sequence Annotation ; *Viral Proteins/genetics/metabolism ; Genomics/methods ; Computational Biology/methods ; Software ; },
abstract = {Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new phages have been identified via metagenomic sequencing, many of them have limited protein function annotation. Accurate function annotation of phage proteins presents several challenges, including their inherent diversity and the scarcity of annotated ones. Existing tools have yet to fully leverage the unique properties of phages in annotating protein functions. In this work, we propose a new protein function annotation tool for phages by leveraging the modular genomic structure of phage genomes. By employing embeddings from the latest protein foundation models and Transformer to capture contextual information between proteins in phage genomes, GOPhage surpasses state-of-the-art methods in annotating diverged proteins and proteins with uncommon functions by 6.78% and 13.05% improvement, respectively. GOPhage can annotate proteins lacking homology search results, which is critical for characterizing the rapidly accumulating phage genomes. We demonstrate the utility of GOPhage by identifying 688 potential holins in phages, which exhibit high structural conservation with known holins. The results show the potential of GOPhage to extend our understanding of newly discovered phages.},
}

*Bacteriophages/genetics
*Genome, Viral
*Molecular Sequence Annotation
*Viral Proteins/genetics/metabolism
Genomics/methods
Computational Biology/methods
Software

@article {pmid39558756,
year = {2025},
author = {Paris, JR and King, RA and Ferrer Obiol, J and Shaw, S and Lange, A and Bourret, V and Hamilton, PB and Rowe, D and Laing, LV and Farbos, A and Moore, K and Urbina, MA and van Aerle, R and Catchen, JM and Wilson, RW and Bury, NR and Santos, EM and Stevens, JR},
title = {The Genomic Signature and Transcriptional Response of Metal Tolerance in Brown Trout Inhabiting Metal-Polluted Rivers.},
journal = {Molecular ecology},
volume = {34},
number = {1},
pages = {e17591},
pmid = {39558756},
issn = {1365-294X},
support = {BB/K003240/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Exeter/ ; WT097835MF/WT_/Wellcome Trust/United Kingdom ; Charityno.1135007,Companyno.06545646//Westcountry Rivers Trust, UK/ ; WT101650MA/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //Environment Agency, UK/ ; },
mesh = {*Genome ; *Transcription, Genetic/drug effects ; *Adaptation, Physiological/drug effects/genetics ; *Rivers ; *Water Pollutants, Chemical/toxicity ; *Salmon/genetics/physiology ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; *Metals/toxicity ; United Kingdom ; Genetic Loci ; Gene Library ; Metagenomics ; Organ Specificity/drug effects ; Gene Ontology ; Animals ; },
abstract = {Industrial pollution is a major driver of ecosystem degradation, but it can also act as a driver of contemporary evolution. As a result of intense mining activity during the Industrial Revolution, several rivers across the southwest of England are polluted with high concentrations of metals. Despite the documented negative impacts of ongoing metal pollution, brown trout (Salmo trutta L.) survive and thrive in many of these metal-impacted rivers. We used population genomics, transcriptomics, and metal burdens to investigate the genomic and transcriptomic signatures of potential metal tolerance. RADseq analysis of six populations (originating from three metal-impacted and three control rivers) revealed strong genetic substructuring between impacted and control populations. We identified selection signatures at 122 loci, including genes related to metal homeostasis and oxidative stress. Trout sampled from metal-impacted rivers exhibited significantly higher tissue concentrations of cadmium, copper, nickel and zinc, which remained elevated after 11 days in metal-free water. After depuration, we used RNAseq to quantify gene expression differences between metal-impacted and control trout, identifying 2042 differentially expressed genes (DEGs) in the gill, and 311 DEGs in the liver. Transcriptomic signatures in the gill were enriched for genes involved in ion transport processes, metal homeostasis, oxidative stress, hypoxia, and response to xenobiotics. Our findings reveal shared genomic and transcriptomic pathways involved in detoxification, oxidative stress responses and ion regulation. Overall, our results demonstrate the diverse effects of metal pollution in shaping both neutral and adaptive genetic variation, whilst also highlighting the potential role of constitutive gene expression in promoting metal tolerance.},
}

*Genome
*Transcription, Genetic/drug effects
*Adaptation, Physiological/drug effects/genetics
*Rivers
*Water Pollutants, Chemical/toxicity
*Salmon/genetics/physiology
Gene Expression Profiling
Gene Expression Regulation/drug effects
*Metals/toxicity
United Kingdom
Genetic Loci
Gene Library
Metagenomics
Organ Specificity/drug effects
Gene Ontology
Animals

@article {pmid39833495,
year = {2025},
author = {Akar, SE and Nwachukwu, W and Adewuyi, OS and Ahumibe, AA and Akanimo, I and Okunromade, O and Babatunde, O and Ihekweazu, C and Hitachi, M and Kato, K and Takamatsu, Y and Hirayama, K and Kaneko, S},
title = {Epidemiology of Yellow Fever in Nigeria: Analysis of Climatic, Ecological, Socio-Demographic, and Clinical Factors Associated with Viral Positivity Among Suspected Cases Using National Surveillance Data, 2017-2023.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {2},
pmid = {39833495},
issn = {2210-6014},
mesh = {Humans ; Nigeria/epidemiology ; *Yellow Fever/epidemiology ; Male ; Female ; Adolescent ; Retrospective Studies ; Adult ; Middle Aged ; Young Adult ; Child ; Child, Preschool ; Infant ; Climate ; Disease Outbreaks/statistics & numerical data ; Yellow fever virus ; Risk Factors ; Socioeconomic Factors ; Sociodemographic Factors ; Population Surveillance/methods ; },
abstract = {BACKGROUND: Since its resurgence in 2017, Yellow fever (YF) outbreaks have continued to occur in Nigeria despite routine immunization and the implementation of several reactive mass vaccinations. Nigeria, Africa's most populous endemic country, is considered a high-priority country for implementing the End Yellow fever Epidemics strategy.

METHODS: This retrospective analysis described the epidemiological profile, trends, and factors associated with Yellow fever viral positivity in Nigeria. We conducted a multivariable binary logistic regression analysis to identify factors associated with YF viral positivity.

RESULTS: Of 16,777 suspected cases, 8532(50.9%) had laboratory confirmation with an overall positivity rate of 6.9%(585). Predictors of YFV positivity were the Jos Plateau, Derived/Guinea Savanah, and the Freshwater/Lowland rainforest compared to the Sahel/Sudan Savannah; dry season compared to rainy season; the hot dry or humid compared to the temperate, dry cool/humid climatic zone; 2019, 2020, 2021, 2022, and 2023 epidemic years compared to compared to 2017; first, third, and fourth quarters compared to the second; male sex compared to female; age group > = 15 years compared to < 15 years; working in outdoor compared to indoor settings; having traveled within the last two weeks; being of unknown vaccination status compared to being vaccinated; and vomiting.

CONCLUSION: Ecological, climatic, and socio-demographic characteristics are drivers of YF outbreaks in Nigeria, and public health interventions need to target these factors to halt local epidemics and reduce the risk of international spread. Inadequate vaccination coverage alone may not account for the recurrent outbreaks of YF in Nigeria.},
}

Humans
Nigeria/epidemiology
*Yellow Fever/epidemiology
Male
Female
Adolescent
Retrospective Studies
Adult
Middle Aged
Young Adult
Child
Child, Preschool
Infant
Climate
Disease Outbreaks/statistics & numerical data
Yellow fever virus
Risk Factors
Socioeconomic Factors
Sociodemographic Factors
Population Surveillance/methods

@article {pmid39833104,
year = {2024},
author = {Liu, F and Zhao, Z and Liu, Y},
title = {PHPGAT: predicting phage hosts based on multimodal heterogeneous knowledge graph with graph attention network.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf017},
pmid = {39833104},
issn = {1477-4054},
support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Natural Science Foundation of Jilin Province, China/ ; },
mesh = {*Bacteriophages/genetics ; Algorithms ; Software ; Computational Biology/methods ; Host-Pathogen Interactions/genetics ; Bacteria/virology/genetics ; Phage Therapy ; },
abstract = {Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity. Accurate prediction of phage hosts is essential for successfully applying phage therapy. However, existing prediction models may not fully encapsulate the complex dynamics of phage-host interactions in diverse microbial environments, indicating a need for improved accuracy through more sophisticated modeling techniques. In response to this challenge, this study introduces a novel phage-host prediction model, PHPGAT, which leverages a multimodal heterogeneous knowledge graph with the advanced GATv2 (Graph Attention Network v2) framework. The model first constructs a multimodal heterogeneous knowledge graph by integrating phage-phage, host-host, and phage-host interactions to capture the intricate connections between biological entities. GATv2 is then employed to extract deep node features and learn dynamic interdependencies, generating context-aware embeddings. Finally, an inner product decoder is designed to compute the likelihood of interaction between a phage and host pair based on the embedding vectors produced by GATv2. Evaluation results using two datasets demonstrate that PHPGAT achieves precise phage host predictions and outperforms other models. PHPGAT is available at https://github.com/ZhaoZMer/PHPGAT.},
}

*Bacteriophages/genetics
Algorithms
Software
Computational Biology/methods
Host-Pathogen Interactions/genetics
Bacteria/virology/genetics
Phage Therapy

@article {pmid39832988,
year = {2025},
author = {Shimels, T and Kantelhardt, EJ and Assefa, M and Fenta, TG},
title = {Spatiotemporal dynamics and prevention strategies of cervical cancer incidence in Addis Ababa, Ethiopia: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {1},
pages = {e089521},
doi = {10.1136/bmjopen-2024-089521},
pmid = {39832988},
issn = {2044-6055},
mesh = {Humans ; Ethiopia/epidemiology ; *Uterine Cervical Neoplasms/epidemiology/prevention & control ; Female ; Incidence ; Adult ; Middle Aged ; *Spatio-Temporal Analysis ; Young Adult ; Bayes Theorem ; Aged ; Geographic Information Systems ; Adolescent ; Papillomavirus Vaccines ; },
abstract = {OBJECTIVE: This study analysed the spatial and temporal patterns of cervical cancer incidence in Addis Ababa from 2012 to 2021.

DESIGN: An ecological study was conducted from 1 September to 30 November 2023 to examine the spatiotemporal trends of cervical cancer incidence.

SETTING: The research was conducted in Addis Ababa, the capital city of Ethiopia.

PARTICIPANTS: Included were all patients with clinically and/or histopathologically confirmed diagnoses of cervical cancer.

DATA ANALYSIS: The study employed advanced analytical tools including R programming, Quantum Geographic Information System V.3.36.0, GeoDa V.1.2.2 and System for Automated Geoscientific Analyses GIS V.9.3.2. Techniques such as Bayesian empirical testing with a block weighting matrix for hotspot identification, Global Moran's I for spatial autocorrelation, nearest neighbour imputation and universal Kriging interpolation were used to manage data gaps. Joinpoint trend analysis and direct age-standardised incidence rate (ASIR) using the Segi's World standard population was applied to compare trends across subcities. A statistical significance threshold was set at p<0.05.

RESULTS: Between 2012 and 2021, a total of 2435 new cervical cancer cases were recorded in the Addis Ababa City Population-based Cancer Registry, with significant spatial clustering observed in Nifas Silk Lafto, Bole, Kirkos as well as parts of Gulele and Yeka sub cities (z score>1.96) in 2018. The citywide age-standardised incidence rate varied from 19 to 26 cases per 100 000 women-years during 2013 and 2016, respectively. Subcity trends varied significantly, with increases and decreases noted in Akaki Kality and Kolfe Keraniyo over different periods while Bole subcity showed modest increase at 4.2% APC (95% CI: 0.6% to 7.9%; p=0.026).

CONCLUSION: The study highlights substantial fluctuations in ASIR and significant geographic disparities in cervical cancer throughout Addis Ababa. To address these challenges, the implementation of school-based human papillomavirus vaccination programmes, alongside targeted interventions, active campaigns and sustained surveillance, is critical. These strategies are essential to effectively reduce the cervical cancer burden and improve health outcomes in the community.},
}

Humans
Ethiopia/epidemiology
*Uterine Cervical Neoplasms/epidemiology/prevention & control
Female
Incidence
Adult
Middle Aged
*Spatio-Temporal Analysis
Young Adult
Bayes Theorem
Aged
Geographic Information Systems
Adolescent
Papillomavirus Vaccines

@article {pmid39832144,
year = {2024},
author = {Ištoňová, M and Dorko, E and Knap, V and Stehlíková, B and Murgová, A and Ondová, P and Rimárová, K},
title = {Assessment of depressive disorders and states of anxiety in patients following cerebrovascular accidents in connection with health care provision.},
journal = {Central European journal of public health},
volume = {32},
number = {Supplement},
pages = {18-24},
pmid = {39832144},
issn = {1210-7778},
mesh = {Humans ; Female ; Male ; Middle Aged ; Aged ; Slovakia/epidemiology ; Aged, 80 and over ; *Stroke/epidemiology/psychology ; Anxiety/epidemiology ; Depressive Disorder/epidemiology ; Surveys and Questionnaires ; Depression/epidemiology ; Anxiety Disorders/epidemiology ; },
abstract = {OBJECTIVE: Anxiety and depression in patients following cerebrovascular accidents are among frequently occurring complications of the medical condition. The consequences affect personal, family, professional, and social life. They cause severe functional and cognitive impairments, limit the ability to perform normal daily activities, which can result in complete disability. The aim of the study was to monitor the occurrence of anxiety and depression in patients following cerebrovascular accidents hospitalized in neurological departments in the region of eastern Slovakia.

METHODS: A total of 101 patients following cerebrovascular accidents, aged from 48-86 years, were included in the descriptive study. Demographic and clinical data were obtained from patients and from medical records. We determined the occurrence of anxiety disorders, depression and emotional distress in patients following cerebrovascular accidents using a standardized Hospital Anxiety and Depression Scale (HADS) questionnaire.

RESULTS: Data analysis confirms a high incidence of anxiety in the HADS-A subscale (9.23 ± 4.13) and depression in the HADS-D subscale (9.09 ± 4.43) during the hospitalization phase of the disease. It demonstrates the pathological occurrence of anxiety states in 37%, depression in 36%, emotional distress in 36%, and a serious degree of combination of pathological values of the anxiety subscale and the depression subscale in 27% of patients. The existence of a strong positive correlation between anxiety and depression indicators was confirmed.

CONCLUSION: The results confirm a high prevalence of anxiety and depression in the acute phase of the disease. The findings indicate that patients recovering from cerebrovascular accidents not only face physical difficulties and loss of independence but also struggle with anxiety and depression, which can negatively impact and slow their recovery. Given the high frequency of these psychological conditions, further research is needed to enhance the quality and effectiveness of care provided to patients with cerebrovascular accidents.},
}

Humans
Female
Male
Middle Aged
Aged
Slovakia/epidemiology
Aged, 80 and over
*Stroke/epidemiology/psychology
Anxiety/epidemiology
Depressive Disorder/epidemiology
Surveys and Questionnaires
Depression/epidemiology
Anxiety Disorders/epidemiology

@article {pmid39832137,
year = {2025},
author = {Iobbi, V and Parisi, V and Giacomini, M and De Riccardis, F and Brun, P and Núñez-Pons, L and Drava, G and Giordani, P and Monti, MC and Poggi, R and Murgia, Y and De Tommasi, N and Bisio, A},
title = {Sesterterpenoids: sources, structural diversity, biological activity, and data management.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00041b},
pmid = {39832137},
issn = {1460-4752},
abstract = {Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.},
}

@article {pmid39830898,
year = {2025},
author = {Gartler, S and Scheer, J and Meyer, A and Abass, K and Bartsch, A and Doloisio, N and Falardeau, J and Hugelius, G and Irrgang, A and Haukur Ingimundarson, J and Jungsberg, L and Lantuit, H and Nymand Larsen, J and Lodi, R and Martin, VS and Mercer, L and Nielsen, D and Overduin, P and Povoroznyuk, O and Rautio, A and Schweitzer, P and Speetjens, NJ and Tomaškovičová, S and Timlin, U and Vanderlinden, JP and Vonk, J and Westerveld, L and Ingeman-Nielsen, T},
title = {A transdisciplinary, comparative analysis reveals key risks from Arctic permafrost thaw.},
journal = {Communications earth & environment},
volume = {6},
number = {1},
pages = {21},
doi = {10.1038/s43247-024-01883-w},
pmid = {39830898},
issn = {2662-4435},
abstract = {Permafrost thaw poses diverse risks to Arctic environments and livelihoods. Understanding the effects of permafrost thaw is vital for informed policymaking and adaptation efforts. Here, we present the consolidated findings of a risk analysis spanning four study regions: Longyearbyen (Svalbard, Norway), the Avannaata municipality (Greenland), the Beaufort Sea region and the Mackenzie River Delta (Canada) and the Bulunskiy District of the Sakha Republic (Russia). Local stakeholders' and scientists' perceptions shaped our understanding of the risks as dynamic, socionatural phenomena involving physical processes, key hazards, and societal consequences. Through an inter- and transdisciplinary risk analysis based on multidirectional knowledge exchanges and thematic network analysis, we identified five key hazards of permafrost thaw. These include infrastructure failure, disruption of mobility and supplies, decreased water quality, challenges for food security, and exposure to diseases and contaminants. The study's novelty resides in the comparative approach spanning different disciplines, environmental and societal contexts, and the transdisciplinary synthesis considering various risk perceptions.},
}

@article {pmid39826720,
year = {2025},
author = {Akhoon, BA and Qiao, Q and Stewart, A and Chen, J and Rodriguez Lopez, CM and Corbin, KR},
title = {Pangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {139980},
doi = {10.1016/j.ijbiomac.2025.139980},
pmid = {39826720},
issn = {1879-0003},
abstract = {Bacterial cellulose (BC) holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges in bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer (HGT) in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters (BGCs), including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.},
}

@article {pmid39817434,
year = {2025},
author = {Blum, J and Brüll, M and Hengstler, JG and Dietrich, DR and Gruber, AJ and Dipalo, M and Kraushaar, U and Mangas, I and Terron, A and Fritsche, E and Marx-Stoelting, P and Hardy, B and Schepky, A and Escher, S and Hartung, T and Landsiedel, R and Odermatt, A and Sachana, M and Koch, K and Dönmez, A and Masjosthusmann, S and Bothe, K and Schildknecht, S and Beilmann, M and Beltman, JB and Fitzpatrick, S and Mangerich, A and Rehm, M and Tangianu, S and Zickgraf, FM and Kamp, H and Burger, G and van de Water, B and Kleinstreuer, N and White, A and Leist, M},
title = {The long way from raw data to NAM-based information: Overview on data layers and processing steps.},
journal = {ALTEX},
volume = {42},
number = {1},
pages = {167-180},
doi = {10.14573/altex.2412171},
pmid = {39817434},
issn = {1868-8551},
abstract = {Toxicological test methods generate raw data and provide instructions on how to use these to determine a final outcome such as a classification of test compounds as hits or non-hits. The data processing pipeline provided in the test method description is often highly complex. Usually, multiple layers of data, ranging from a machine-generated output to the final hit definition, are considered. Transition between each of these layers often requires several data processing steps. As changes in any of these processing steps can impact the final output of new approach methods (NAMs), the processing pipeline is an essential part of a NAM description and should be included in reporting templates such as the ToxTemp. The same raw data, processed in different ways, may result in different final outcomes that may affect the readiness status and regulatory acceptance of the NAM, as an altered output can affect robustness, performance, and relevance. Data management, pro­cessing, and interpretation are therefore important elements of a comprehensive NAM definition. We aim to give an overview of the most important data levels to be considered during the devel­opment and application of a NAM. In addition, we illustrate data processing and evaluation steps between these data levels. As NAMs are increasingly standard components of the spectrum of toxi­cological test methods used for risk assessment, awareness of the significance of data processing steps in NAMs is crucial for building trust, ensuring acceptance, and fostering the reproducibility of NAM outcomes.},
}

@article {pmid39652873,
year = {2025},
author = {Naderian, M and Norland, K and Schaid, DJ and Kullo, IJ},
title = {Development and Evaluation of a Comprehensive Prediction Model for Incident Coronary Heart Disease Using Genetic, Social, and Lifestyle-Psychological Factors: A Prospective Analysis of the UK Biobank.},
journal = {Annals of internal medicine},
volume = {178},
number = {1},
pages = {1-10},
doi = {10.7326/ANNALS-24-00716},
pmid = {39652873},
issn = {1539-3704},
mesh = {Humans ; Male ; United Kingdom/epidemiology ; Middle Aged ; *Coronary Disease/epidemiology ; Female ; Prospective Studies ; Risk Assessment ; *Life Style ; Risk Factors ; Incidence ; Social Determinants of Health ; Machine Learning ; UK Biobank ; },
abstract = {BACKGROUND: Clinical risk calculators for coronary heart disease (CHD) do not include genetic, social, and lifestyle-psychological risk factors.

OBJECTIVE: To improve CHD risk prediction by developing and evaluating a prediction model that incorporated a polygenic risk score (PRS) and a polysocial score (PSS), the latter including social determinants of health and lifestyle-psychological factors.

DESIGN: Cohort study.

SETTING: United Kingdom.

PARTICIPANTS: UK Biobank participants recruited between 2006 and 2010.

MEASUREMENTS: Incident CHD (myocardial infarction and/or coronary revascularization); 10-year clinical risk based on pooled cohort equations (PCE), Predicting Risk of cardiovascular disease EVENTs (PREVENT), and QRISK3; PRS (Polygenic Score Catalog identification: PGS000018) for CHD (PRSCHD); and PSSCHD from 100 related covariates. Machine-learning and time-to-event analyses and model performance indices.

RESULTS: In 388 224 participants (age, 55.5 [SD, 8.1] years; 42.5% men; 94.9% White), the hazard ratio for 1 SD increase in PSSCHD for incident CHD was 1.43 (95% CI, 1.38 to 1.49; P < 0.001) and for 1 SD increase in PRSCHD was 1.59 (CI, 1.53 to 1.66, P < 0.001). Non-White persons had higher PSSCHD than White persons. The effects of PSSCHD and PRSCHD on CHD were independent and additive. At a 10-year CHD risk threshold of 7.5%, adding PSSCHD and PRSCHD to PCE reclassified 12% of participants, with 1.86 times higher CHD risk in the up- versus down-reclassified persons and showed superior performance compared with PCE as reflected by improved net benefit while maintaining good calibration relative to the clinical risk calculators. Similar results were seen when incorporating PSSCHD and PRSCHD into PREVENT and QRISK3.

LIMITATION: A predominantly White cohort; possible healthy participant effect and ecological fallacy.

CONCLUSION: A PSSCHD was associated with incident CHD and its joint modeling with PRSCHD improved the performance of clinical risk calculators.

PRIMARY FUNDING SOURCE: National Human Genome Research Institute.},
}

Humans
Male
United Kingdom/epidemiology
Middle Aged
*Coronary Disease/epidemiology
Female
Prospective Studies
Risk Assessment
*Life Style
Risk Factors
Incidence
Social Determinants of Health
Machine Learning
UK Biobank

@article {pmid39830091,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Golden Y, Autographa pulchrina (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {375},
doi = {10.12688/wellcomeopenres.19840.1},
pmid = {39830091},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Autographa pulchrina (the Beautiful Golden Y; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 426.2 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,916 protein coding genes.},
}

@article {pmid39825388,
year = {2025},
author = {Burthe, SJ and Kumbar, B and Schäfer, SM and Purse, BV and Vanak, AT and Balakrishnan, N and Hassall, R and Hoti, SL and Narayanaswamy, D and Potadar, S and Rahman, M and Chanda, MM},
title = {First evidence of transovarial transmission of Kyasanur Forest disease virus in Haemaphysalis and Rhipicephalus ticks in the wild.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {14},
pmid = {39825388},
issn = {1756-3305},
support = {MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/P024335/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; MR/T029846/1//Global Challenges Research Fund/ ; },
mesh = {Animals ; Female ; *Encephalitis Viruses, Tick-Borne/physiology/isolation & purification/genetics ; *Kyasanur Forest Disease/transmission/virology ; India/epidemiology ; *Larva/virology ; *Rhipicephalus/virology ; *Ixodidae/virology ; Arachnid Vectors/virology ; },
abstract = {BACKGROUND: Kyasanur forest disease virus (KFDV) is a tick-borne flavivirus causing debilitating and potentially fatal disease in people in the Western Ghats region of India. The transmission cycle is complex, involving multiple vector and host species, but there are significant gaps in ecological knowledge. Empirical data on pathogen-vector-host interactions and incrimination have not been updated since the last century, despite significant local changes in land use and the expansion of KFD to new areas. Mathematical models predict that transovarial transmission, whereby adult female ticks pass KFDV infections to their offspring, plays an important role in the persistence of KFD, but this has not been shown in the wild. Here we set out to establish whether transovarial transmission of KFDV was occurring under natural field conditions by assessing whether host-seeking larvae were positive for KFDV.

METHODS: Ticks were sampled by dragging and flagging across a broad range of habitats within the agro-forest matrix at 49 sites in two districts: Shivamogga, Karnataka and Wayanad, Kerala (September 2018-March 2019), and larvae were tested for KFDV by PCR.

RESULTS: In total, larval ticks from 7 of the 49 sites sampled tested positive for KFDV, indicating that transovarial transmission is occurring. Of the 13 KFDV-positive larval samples, 3 came from around houses and gardens, 5 from crops (3 from harvested rice paddy and 2 from areca plantation), 1 from teak plantation and 4 (2 from 1 transect) from forests. Five different tick species were found to have KFDV-positive larvae: Haemaphysalis spinigera, H. bispinosa, Rhipicephalus annulatus, R. microplus and an unidentifiable species of Haemaphysalis (no close match in GenBank).

CONCLUSIONS: Our empirical confirmation of transovarial transmission has important implications for understanding and predicting KFD dynamics, suggesting that ticks may act as a reservoir for KFDV. Moreover, small mammals and cattle may play crucial roles in transmission if small mammals are the main hosts for larvae infected via transovarial transmission, and cattle support large numbers of infected female adult ticks. This first report of transovarial transmission of KFDV, and within a hitherto undescribed range of vectors and habitats, will help disease managers improve KFD surveillance and mitigation strategies, ultimately leading to communities becoming more resilient to the risk of this tick-transmitted disease.},
}

Animals
Female
*Encephalitis Viruses, Tick-Borne/physiology/isolation & purification/genetics
*Kyasanur Forest Disease/transmission/virology
India/epidemiology
*Larva/virology
*Rhipicephalus/virology
*Ixodidae/virology
Arachnid Vectors/virology

@article {pmid39441382,
year = {2025},
author = {Canzler, S and Schubert, K and Rolle-Kampczyk, UE and Wang, Z and Schreiber, S and Seitz, H and Mockly, S and Kamp, H and Haake, V and Huisinga, M and Bergen, MV and Buesen, R and Hackermüller, J},
title = {Evaluating the performance of multi-omics integration: a thyroid toxicity case study.},
journal = {Archives of toxicology},
volume = {99},
number = {1},
pages = {309-332},
pmid = {39441382},
issn = {1432-0738},
support = {C5 - XomeTox//European Chemical Industry Council/ ; 101057014//HORIZON EUROPE Framework Programme/ ; },
mesh = {Animals ; *Thyroid Gland/drug effects/pathology ; *Propylthiouracil/toxicity ; Rats ; Metabolomics ; Proteomics ; Transcriptome/drug effects ; Male ; Genomics ; Risk Assessment ; Female ; Antithyroid Agents/toxicity ; Rats, Sprague-Dawley ; Proteome/metabolism ; Multiomics ; },
abstract = {Multi-omics data integration has been repeatedly discussed as the way forward to more comprehensively cover the molecular responses of cells or organisms to chemical exposure in systems toxicology and regulatory risk assessment. In Canzler et al. (Arch Toxicol 94(2):371-388. https://doi.org/10.1007/s00204-020-02656-y), we reviewed the state of the art in applying multi-omics approaches in toxicological research and chemical risk assessment. We developed best practices for the experimental design of multi-omics studies, omics data acquisition, and subsequent omics data integration. We found that multi-omics data sets for toxicological research questions were generally rare, with no data sets comprising more than two omics layers adhering to these best practices. Due to these limitations, we could not fully assess the benefits of different data integration approaches or quantitatively evaluate the contribution of various omics layers for toxicological research questions. Here, we report on a multi-omics study on thyroid toxicity that we conducted in compliance with these best practices. We induced direct and indirect thyroid toxicity through Propylthiouracil (PTU) and Phenytoin, respectively, in a 28-day plus 14-day recovery oral rat toxicity study. We collected clinical and histopathological data and six omics layers, including the long and short transcriptome, proteome, phosphoproteome, and metabolome from plasma, thyroid, and liver. We demonstrate that the multi-omics approach is superior to single-omics in detecting responses at the regulatory pathway level. We also show how combining omics data with clinical and histopathological parameters facilitates the interpretation of the data. Furthermore, we illustrate how multi-omics integration can hint at the involvement of non-coding RNAs in post-transcriptional regulation. Also, we show that multi-omics facilitates grouping, and we assess how much information individual and combinations of omics layers contribute to this approach.},
}

Animals
*Thyroid Gland/drug effects/pathology
*Propylthiouracil/toxicity
Rats
Metabolomics
Proteomics
Transcriptome/drug effects
Male
Genomics
Risk Assessment
Female
Antithyroid Agents/toxicity
Rats, Sprague-Dawley
Proteome/metabolism
Multiomics

@article {pmid39822595,
year = {2024},
author = {Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Poplar Grey moth, Subacronicta megacephala (Denis & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {696},
doi = {10.12688/wellcomeopenres.23371.1},
pmid = {39822595},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Subacronicta megacephala (Poplar Grey moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 424.20 megabases. Most of the assembly (99.02%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,189 protein-coding genes.},
}

@article {pmid39822261,
year = {2025},
author = {Proença Neto, MA and De Sousa, MPA},
title = {Pytaxon: A Python software for resolving and correcting taxonomic names in biodiversity data.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e138257},
doi = {10.3897/BDJ.13.e138257},
pmid = {39822261},
issn = {1314-2828},
abstract = {BACKGROUND: The standardisation and correction of taxonomic names in large biodiversity databases remain persistent challenges for researchers, as errors in species names can compromise ecological analyses, land-use planning and conservation efforts, particularly when inaccurate data are shared on global biodiversity portals.

NEW INFORMATION: We present pytaxon, a Python software designed to resolve and correct taxonomic names in biodiversity data by leveraging the Global Names Verifier (GNV) API and employing fuzzy matching techniques to suggest corrections for discrepancies and nomenclatural inconsistencies. The pytaxon offers both a Command Line Interface (CLI) and a Graphical User Interface (GUI), ensuring accessibility to users with different levels of computing expertise. Tests on spreadsheets derived from datasets published in the Global Biodiversity Information Facility (GBIF) demonstrated its effectiveness in identifying and resolving taxonomic errors. By mitigating the propagation of inaccuracies from researchers' datasets to global biodiversity databases, pytaxon supports more reliable conservation decisions and robust scientific investigations. Its contributions enhance data integrity and promote informed biodiversity management in a rapidly evolving global environment.},
}

@article {pmid39821365,
year = {2025},
author = {Zhang, D and Cai, Y and Sun, Y and Zeng, P and Wang, W and Wang, W and Jiang, X and Lian, Y},
title = {A Real-World Disproportionality Analysis of Histamine H2-Receptors Antagonists (Famotidine): A Pharmacovigilance Study Based on Spontaneous Reports in the FDA Adverse Event Reporting System.},
journal = {Drug development research},
volume = {86},
number = {1},
pages = {e70045},
doi = {10.1002/ddr.70045},
pmid = {39821365},
issn = {1098-2299},
support = {//This study was funded by the National Natural Science Foundation of China (Grant No: 82303109), the Natural Science Foundation of Fujian Province, China (Grant No: 2022J05299), Cross-Strait Postdoctoral Exchange Funding Program of Fujian Province, China (Grant No: 2021B002)./ ; },
mesh = {Humans ; *Famotidine/adverse effects ; *Adverse Drug Reaction Reporting Systems/statistics & numerical data ; United States/epidemiology ; *Histamine H2 Antagonists/adverse effects ; *Pharmacovigilance ; *United States Food and Drug Administration ; Female ; Male ; Adult ; Middle Aged ; Aged ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Databases, Factual ; Infant ; },
abstract = {Famotidine is an H2 receptor antagonist and is currently used on a large scale in gastroenterology. However, Famotidine may also cause severe toxicity to organ systems, including the blood system, digestive system, and urinary system. The objective of this study was to scientifically and systematically investigate the adverse events (AEs) of Famotidine in the real world through the FDA Adverse Event Reporting System (FAERS) database. A disproportionality analysis was used to quantify the signals of AEs associated with Famotidine in FAERS data from the first quarter of 2004 to the first quarter of 2023. The clinical features, onset time, oral and intravenous administration and severe consequences of Famotidine induced AEs were further analyzed. Among the four tests, we found several AEs that were not mentioned in the drug label. For example, abdominal pain upper, abdominal discomfort, dyspepsia, liver disorder, gastrooesophageal reflux disease, and rhabdomyolysis. These AEs are consistent with the drug instructions. Interestingly, we found several unreported AEs, such as: cerebral infarction, hypocalcaemia, hallucination, visual, hypomagnesaemia, hypoparathyroidism, diabetes insipidus, vulvovaginal candidiasis, retro-orbital neoplasm, neuroblastoma recurrent, and malignant cranial nerve neoplasm. Most of our findings are consistent with clinical observations and drug labels, and we also found possible new and unexpected AEs signals, which suggest the need for prospective clinical studies to confirm these results and explain their relationships. Our findings provide valuable evidence for further safety studies.},
}

Humans
*Famotidine/adverse effects
*Adverse Drug Reaction Reporting Systems/statistics & numerical data
United States/epidemiology
*Histamine H2 Antagonists/adverse effects
*Pharmacovigilance
*United States Food and Drug Administration
Female
Male
Adult
Middle Aged
Aged
Adolescent
Young Adult
Child
Child, Preschool
Drug-Related Side Effects and Adverse Reactions/epidemiology
Databases, Factual
Infant

@article {pmid39423319,
year = {2025},
author = {Tian, Y and Yang, L and Ding, S and Zhang, D and Yuan, L and Liu, Z and Hu, QN},
title = {BioTRY: A Comprehensive Knowledge Base for Titer, Rate, and Yield of Biosynthesis.},
journal = {ACS synthetic biology},
volume = {14},
number = {1},
pages = {285-289},
doi = {10.1021/acssynbio.4c00347},
pmid = {39423319},
issn = {2161-5063},
mesh = {*Synthetic Biology/methods ; *Knowledge Bases ; Databases, Factual ; Software ; Computational Biology/methods ; },
abstract = {Synthetic biology is rapidly evolving into a data-intensive science that increasingly relies on massive data sets; one of its applications is the evaluation of the economic viability of fermentation processes. However, the key economic indicators, namely titer, rate, and yield (TRY), which respectively reflect the downstream processing, reactor size, and raw material costs, are not well captured in bioinformatics databases. In this paper, we present BioTRY, an intuitive and user-friendly tool that contains >5,000 biochemicals and >3,800 strains, along with over 52,000 corresponding TRY entries with original references. It is freely available at http://www.synbiohealth.cn/biotry. To our knowledge, BioTRY is the first available database on biosynthesis TRY data from original research. We anticipate that BioTRY will become a useful tool that aids researchers and decision-makers in understanding the current development state of biosynthesis and allows them to foresee potential prospects and applications for biosynthesis.},
}

*Synthetic Biology/methods
*Knowledge Bases
Databases, Factual
Software
Computational Biology/methods

@article {pmid38383603,
year = {2025},
author = {Nevers, Y and Warwick Vesztrocy, A and Rossier, V and Train, CM and Altenhoff, A and Dessimoz, C and Glover, NM},
title = {Quality assessment of gene repertoire annotations with OMArk.},
journal = {Nature biotechnology},
volume = {43},
number = {1},
pages = {124-133},
pmid = {38383603},
issn = {1546-1696},
mesh = {*Software ; *Molecular Sequence Annotation ; *Proteome/genetics ; Animals ; Databases, Protein ; Genomics/methods ; },
abstract = {In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.},
}

*Software
*Molecular Sequence Annotation
*Proteome/genetics
Animals
Databases, Protein
Genomics/methods

@article {pmid39814778,
year = {2025},
author = {Gómez-Gras, D and Linares, C and Viladrich, N and Zentner, Y and Grinyó, J and Gori, A and McFadden, CS and Fabricius, KE and Madin, JS},
title = {The Octocoral Trait Database: a global database of trait information for octocoral species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {82},
pmid = {39814778},
issn = {2052-4463},
mesh = {*Anthozoa/classification ; Animals ; *Databases, Factual ; *Coral Reefs ; Biodiversity ; Ecosystem ; },
abstract = {Trait-based approaches are revolutionizing our understanding of high-diversity ecosystems by providing insights into the principles underlying key ecological processes, such as community assembly, species distribution, resilience, and the relationship between biodiversity and ecosystem functioning. In 2016, the Coral Trait Database advanced coral reef science by centralizing trait information for stony corals (i.e., Subphylum Anthozoa, Class Hexacorallia, Order Scleractinia). However, the absence of trait data for soft corals, gorgonians, and sea pens (i.e., Class Octocorallia) limits our understanding of ecosystems where these organisms are significant members and play pivotal roles. To address this gap, we introduce the Octocoral Trait Database, a global, open-source database of curated trait data for octocorals. This database houses species- and individual-level data, complemented by contextual information that provides a relevant framework for analyses. The inaugural dataset, OctocoralTraits v2.2, contains over 97,500 global trait observations across 98 traits and over 3,500 species. The database aims to evolve into a steadily growing, community-led resource that advances future marine science, with a particular emphasis on coral reef research.},
}

*Anthozoa/classification
Animals
*Databases, Factual
*Coral Reefs
Biodiversity
Ecosystem

@article {pmid39813953,
year = {2025},
author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL},
title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109260},
doi = {10.1016/j.envint.2025.109260},
pmid = {39813953},
issn = {1873-6750},
abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.},
}

@article {pmid39813347,
year = {2025},
author = {Gu, S and Shao, Z and Qu, Z and Zhu, S and Shao, Y and Zhang, D and Allen, R and He, R and Shao, J and Xiong, G and Jousset, A and Friman, VP and Wei, Z and Kümmerli, R and Li, Z},
title = {Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq5038},
doi = {10.1126/sciadv.adq5038},
pmid = {39813347},
issn = {2375-2548},
mesh = {*Iron/metabolism ; *Siderophores/metabolism ; *Evolution, Molecular ; Ecosystem ; Pseudomonas/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Ligases/metabolism/genetics ; Humans ; Computational Biology/methods ; Bacterial Outer Membrane Proteins ; Receptors, Cell Surface ; },
abstract = {Bacterial social interactions play crucial roles in various ecological, medical, and biotechnological contexts. However, predicting these interactions from genome sequences is notoriously difficult. Here, we developed bioinformatic tools to predict whether secreted iron-scavenging siderophores stimulate or inhibit the growth of community members. Siderophores are chemically diverse and can be stimulatory or inhibitory depending on whether bacteria have or lack corresponding uptake receptors. We focused on 1928 representative Pseudomonas genomes and developed an experimentally validated coevolution algorithm to match encoded siderophore synthetases to corresponding receptor groups. We derived community-level iron interaction networks to show that siderophore-mediated interactions differ across habitats and lifestyles. Specifically, dense networks of siderophore sharing and competition were observed among environmental and nonpathogenic species, while small, fragmented networks occurred among human-associated and pathogenic species. Together, our sequence-to-ecology approach empowers the analyses of social interactions among thousands of bacterial strains and offers opportunities for targeted intervention to microbial communities.},
}

*Iron/metabolism
*Siderophores/metabolism
*Evolution, Molecular
Ecosystem
Pseudomonas/genetics/metabolism
Bacterial Proteins/genetics/metabolism
Genome, Bacterial
Ligases/metabolism/genetics
Humans
Computational Biology/methods
Bacterial Outer Membrane Proteins
Receptors, Cell Surface

@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