@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020330},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@article {pmid41597522,
year = {2025},
author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T},
title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010002},
pmid = {41597522},
issn = {2076-2607},
support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; },
abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.},
}

@article {pmid41597405,
year = {2026},
author = {Sekulic, M and Stepovic, M and Sorak, M and Mijailovic, S and Rajkovic Pavlovic, Z and Vulovic, M and Radmanovic, O and Radmanovic, B and Vuckovic Filipovic, J and Gavrilovic, J and Jovanovic, B and Spasic, B and Folic, N and Rosic, V and Dragicevic, T and Markovic, V},
title = {Elevated Blood Pressure and Risk Factors in 19-Year-Olds in Serbia: A Cross-Sectional Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {1},
pages = {},
doi = {10.3390/medicina62010119},
pmid = {41597405},
issn = {1648-9144},
mesh = {Humans ; Male ; Serbia/epidemiology ; Cross-Sectional Studies ; Female ; *Hypertension/epidemiology ; Risk Factors ; Young Adult ; Logistic Models ; Surveys and Questionnaires ; Feeding Behavior ; Blood Pressure/physiology ; Adult ; Prevalence ; },
abstract = {Background and Objectives: Hypertension in young adulthood is increasingly recognized as a precursor to future cardiovascular disease. Early identification of modifiable risk factors, such as dietary habits, lifestyle behaviors, and psychological indicators, is critical for prevention. This study aimed to examine the elevated clinic blood pressure and associated factors in 19-year-old individuals in Serbia. Materials and Methods: A cross-sectional study was conducted using data from the 2019 Fourth National Health Survey. A total of 212 participants underwent blood pressure measurement, anthropometric assessment, and completed standardized questionnaires on diet, physical activity, depressive symptoms, and sociodemographic characteristics. Blood pressure was classified according to ESC/ESH guidelines. Associations with elevated blood pressure were assessed using chi-square tests and multivariate logistic regression. Results: Most participants had optimal or normal blood pressure, while 18.9% had elevated blood pressure, including high-normal and Grade I-II hypertension. Elevated blood pressure was more prevalent among males and was associated with depressive symptoms. Nutrition status was significantly associated with elevated blood pressure, and some dietary habits like consumption of pure fruit or vegetable juices and the intake of processed meat products. Other socioeconomic factors, eating habits and physical activity were not significantly correlated. In multivariate logistic regression, elevated arterial blood pressure was significantly associated with consuming pure fruit or vegetable juices less than once per week (OR = 3.239; 95% CI: 1.413-7.427) and with consuming processed meat products several times per week in comparison to the daily consumption (OR = 0.325; 95% CI: 0.130-0.812), while no other variables remained statistically significant. Conclusions: Clinically elevated arterial blood pressure is present in a substantial proportion of 19-year-olds. Early lifestyle interventions targeting nutrition and psychological health may prevent progression to hypertension and reduce long-term cardiovascular risk.},
}

Humans
Male
Serbia/epidemiology
Cross-Sectional Studies
Female
*Hypertension/epidemiology
Risk Factors
Young Adult
Logistic Models
Surveys and Questionnaires
Feeding Behavior
Blood Pressure/physiology
Adult
Prevalence

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41596699,
year = {2026},
author = {Wang, R and Gu, C and Li, H and Wang, L and Sun, R and Fu, K and Shi, W and Wan, X},
title = {Multi-Omics Profiling of the Hepatopancreas of Ridgetail White Prawn Exopalaemon carinicauda Under Sulfate Stress.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021056},
pmid = {41596699},
issn = {1422-0067},
support = {JC2023085//The Nantong City Natural Science Foundation Project/ ; },
mesh = {Animals ; *Palaemonidae/metabolism/genetics/drug effects ; *Hepatopancreas/metabolism/drug effects/ultrastructure ; *Sulfates/toxicity ; Proteomics/methods ; *Stress, Physiological ; Transcriptome ; Multiomics ; },
abstract = {With intensifying global climate change and human activities, and with regional topography interactions, soil and water salinization has intensified, posing major ecological and environmental challenges worldwide. Here, we integrated histology, transmission electron microscopy, RNA sequencing (RNA-seq) and data-independent acquisition (DIA)-based proteomics to profile hepatopancreas responses of Exopalaemon carinicauda during acute sulfate stress (≤48 h). Sulfate exposure disrupted tubular architecture and organelle integrity, consistent with early cellular injury. Multi-omics analyses revealed metabolic reprogramming marked by suppressed glycolysis (e.g., HK2, ENO) and enhanced oxidative phosphorylation (e.g., ATP5F1B), together with activation of calcium signaling (e.g., SLC8A1, ADCY9) and reinforcement of antioxidant/one-carbon and glucose-branch pathways (e.g., SHMT2, PGAM2). These coordinated transcript-protein changes indicate a shift from rapid cytosolic ATP supply to mitochondrial ATP production while buffering Ca[2+] overload and reactive oxygen species. Collectively, our results delineate the physiological and molecular adjustments that enable E. carinicauda to cope with sulfate conditions and provide mechanistic targets for selective breeding and water-quality management in saline-alkaline aquaculture.},
}

Animals
*Palaemonidae/metabolism/genetics/drug effects
*Hepatopancreas/metabolism/drug effects/ultrastructure
*Sulfates/toxicity
Proteomics/methods
*Stress, Physiological
Transcriptome
Multiomics

@article {pmid41595990,
year = {2026},
author = {Ha, S and Lee, T and Seo, H and Yoon, S and Lee, H},
title = {A Selective RAG-Enhanced Hybrid ML-LLM Framework for Efficient and Explainable Fatigue Prediction Using Wearable Sensor Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/bioengineering13010058},
pmid = {41595990},
issn = {2306-5354},
support = {RS-2024-00457381//National Research Foundation of Korea/ ; RS-2024-00440371//National Research Foundation of Korea/ ; },
abstract = {Fatigue is a multifactorial phenomenon affecting both physical and psychological performance, particularly in high-stress occupations. Although wearable sensors enable continuous monitoring, conventional machine-learning (ML) models can produce unstable, weakly calibrated, and opaque predictions in real-world settings. To improve reliability and interpretability, we developed a selective Retrieval-Augmented Generation (RAG)-enhanced hybrid ML-LLM framework that integrates the efficiency of ML with the reasoning capability of large language models (LLMs). Using wearable and ecological momentary assessment data from 297 emergency responders (9543 seven-day windows), logistic regression, XGBoost, and LSTM models were trained to classify fatigue levels dichotomized by the median of daily tiredness scores. The LLM was selectively activated only for borderline ML outputs (0.45 ≤ p ≤ 0.55), using symbolic rules and retrieved analog examples. In the uncertainty region, performance improved from 0.556/0.684/0.635/0.659 to 0.617/0.703/0.748/0.725 (accuracy/precision/recall/F1). On the full test set, performance similarly improved from 0.707/0.739/0.918/0.819 to 0.718/0.741/0.937/0.827, with gains confirmed by McNemar's paired comparison test (p < 0.05). SHAP-based ML interpretation and LLM reasoning analyses independently identified short-term sleep duration and heart-rate variability as dominant predictors, providing transparent explanations for model behavior. This framework enhances classification robustness, interpretability, and efficiency, offering a scalable solution for real-world fatigue monitoring.},
}

@article {pmid41595397,
year = {2026},
author = {Jean-Baptiste, CO},
title = {A Prevention-Focused Geospatial Epidemiology Framework for Identifying Multilevel Vulnerability Across Diverse Settings.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/healthcare14020261},
pmid = {41595397},
issn = {2227-9032},
abstract = {Background/Objectives: Geographic Information Systems (GIS) offer essential capabilities for identifying spatial concentrations of vulnerability and strengthening context-aware prevention strategies. This manuscript describes a geospatial architecture designed to generate anticipatory, place-based risk identification applicable across diverse community and institutional environments. Interpersonal Violence (IPV), one of several preventable harms that benefit from this spatially informed analysis, remains a critical public health challenge shaped by structural, ecological, and situational factors. Methods: The conceptual framework presented integrates de-identified surveillance data, ecological indicators, environmental and temporal dynamics into a unified spatial epidemiological model. Multilevel data layers are geocoded, spatially matched, and analyzed using clustering (e.g., Getis-Ord Gi*), spatial dependence metrics (e.g., Moran's I), and contextual modeling to support anticipatory identification of elevated vulnerability. Framework Outputs: The model is designed to identify spatial clustering, mobility-linked risk patterns, and emerging escalation zones using neighborhood disadvantage, built-environment factors, and situational markers. Outputs are intended to support both clinical decision-making (e.g., geocoded trauma screening, and context-aware discharge planning), and community-level prevention (e.g., targeted environmental interventions and cross-sector resource coordination). Conclusions: This framework synthesizes behavioral theory, spatial epidemiology, and prevention science into an integrative architecture for coordinated public health response. As a conceptual foundation for future empirical research, it advances the development of more dynamic, spatially informed, and equity-focused prevention systems.},
}

@article {pmid41593706,
year = {2026},
author = {Gothe, S and Jagtap, S and Böhmer, P and Reuter, M and Frank, S and Sreenu, VB and Bell-Sakyi, L and Merits, A and Altinli, M and Schnettler, E},
title = {Characterization of Culex pipiens cell lines: virus infection and RNAi response.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07248-w},
pmid = {41593706},
issn = {1756-3305},
support = {Culifo3//BMLE/ ; TTU 01.708//Deutsches Zentrum für Infektionsforschung/ ; TTU 01.701 and TTU 01.708//Deutsches Zentrum für Infektionsforschung/ ; 500072465//Deutsche Forschungsgemeinschaft/ ; 497659464//Deutsche Forschungsgemeinschaft/ ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; GSO KT/24//Klaus Tschira Stiftung/ ; },
abstract = {BACKGROUND: Arboviruses transmitted by mosquitoes pose a global health threat, causing diseases ranging from mild fevers to severe encephalitis and hemorrhagic fevers. Despite their growing impact, arbovirus research is hindered by biosafety constraints and the need of specialized BSL-3 insectariums. To circumvent these challenges, mosquito-derived cell lines have become indispensable tools for investigating virus-vector interactions. However, most available cell lines originate from Aedes and Anopheles spp., creating a critical research gap for other key vectors such as Culex spp. Although a few cell lines were previously established, they did not represent primary transmitters of West Nile virus (WNV) and other emerging arboviruses in Europe, such as Culex pipiens.

METHODS: To address this gap, the current study aimed to characterize two recently established Culex pipiens cell lines: CPE/LULS50 (Culex pipiens pipiens & molestus) and CPL/LULS56 (Culex pipiens molestus) in more detail including testing their virus susceptibility, antiviral RNAi response, and possible presence of insect-specific viruses.

RESULTS: The replication of arboviruses from three clinically relevant families (Flaviviridae, Peribunyaviridae, and Togaviridae), as well as insect-specific viruses, was observed in both CPE/LULS50 and CPL/LULS56 cell lines. Furthermore, small RNA profiling revealed production of virus-specific small interfering RNA (siRNA) in both cell lines for all tested viruses. Interestingly, virus-specific PIWI-interacting RNA (piRNA) was only detected for the Peribunyaviridae.

CONCLUSIONS: The current study demonstrates that the CPE/LULS50 and CPL/LULS56 cell lines are suitable candidates to facilitate research into Culex-specific virus-vector interactions, ultimately contributing to mitigation of the impact of Culex-borne arboviruses on public health.},
}

@article {pmid41593685,
year = {2026},
author = {Naserrudin, NA and Rahman, AB and Manah, AM and Donnie, EM and Jamaji, L and Lin, PYP and Miller, A and Krishnan, M and Hassan, MR},
title = {What does monkey malaria mean to you? A participatory photovoice study in rural Malaysian Borneo.},
journal = {Malaria journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12936-026-05797-0},
pmid = {41593685},
issn = {1475-2875},
abstract = {BACKGROUND: Zoonotic (monkey) malaria, caused by Plasmodium knowlesi, is an escalating concern in Sabah, Malaysia, where humans, macaques and mosquito vectors share overlapping ecosystems. Conventional research methods often overlook how affected communities perceive and respond to this risk within their cultural and environmental contexts. This study uses photovoice, a participatory visual method to explore the question 'What does monkey malaria mean to you? and to elevate community voices in guiding locally relevant disease prevention strategies.

METHODS: From January to May 2024, twenty participants aged 18 to 62 from three rural Sabah villages captured photographs over a 20-day period using their smartphones to document their experiences and perceptions on monkey malaria. Follow-up focus group discussions (FGDs) enabled participants to collectively reflect on and interpret their images. Reflexive thematic analysis was applied to the visual and verbal data and findings. Digital tools supported coordination and data management without replacing the participant-researcher engagement.

RESULTS: Five interrelated themes were generated: (1) monkey malaria as an embedded, everyday risk, (2) community resilience manifested through locally derived practices, (3) structural and socio-ecological challenges shaping exposure, (4) the interface of human, wildlife, and environmental health, (5) cultural knowledge and blended practices for coping with malaria risk. Participants articulated how landscape features, economic dependence on forested and plantation areas, and daily routines collectively structure risk, reflecting a dynamic 'landscape of risk'. They also expressed aspirations for collaborative and culturally appropriate strategies.

CONCLUSION: Using photovoice, participants described how malaria risk is part of their everyday lives, the coping strategies they use and the social and environmental conditions that influence their understanding. By prioritising community voices, the findings show that effective malaria control should go beyond strictly biomedical models to include local priorities, cultural practices and lived experience. Photovoice generated deep insights grounded in the community context and encouraged meaningful participation, providing useful guidance for designing intervention strategies that are culturally appropriate and more sustainable.},
}

@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
Microbiota/genetics
Environmental Pollutants/metabolism
Metagenome
Metagenomics

@article {pmid41591842,
year = {2026},
author = {Islam, H and Sharma, A and Blair, J and Lopatkin, AJ},
title = {PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/nar/gkaf1507},
pmid = {41591842},
issn = {1362-4962},
support = {1R35GM150871-01/NH/NIH HHS/United States ; //Pew Charitable Trusts Foundation/ ; 2440082//National Science Foundation/ ; //Edward Mallinckrodt Jr. Foundation/ ; },
mesh = {*Plasmids/genetics ; *Molecular Sequence Annotation/methods ; *Databases, Genetic ; Genome, Bacterial ; Software ; DNA Transposable Elements ; Genes, Bacterial ; Bacteria/genetics ; },
abstract = {Conjugative plasmids are key drivers of bacterial adaptation, enabling the horizontal transfer of accessory genes within and across diverse microbial populations, yet annotating them remains challenging due to their highly mosaic genetic architectures and inconsistent gene naming conventions that complicate functional predictions and comparative analyses. To address this, we developed PlasAnn, a database designed specifically for genes encoded on natural plasmids, paired with a dedicated annotation pipeline (available via Bioconda or through the URL https://plasann.rochester.edu/). The curated database provides highly accurate, plasmid-type-specific gene names with standardized functional annotations, enabling direct comparison across plasmids without manual curation or specialized expertise, while the integrated annotation tool incorporates other common plasmid features for a fast, one-stop solution that outperforms broad prokaryotic genome annotation pipelines in both accuracy and efficiency. We demonstrate PlasAnn's utility by showing that plasmid accessory genes from different groups often share conserved repertoires, suggesting dynamic, modular networks of interconnected genes, and by revealing that plasmid-encoded transposable elements frequently carry genes related to bacterial adaptation beyond antibiotic resistance, including metabolism, virulence, and stress responses, emphasizing their broader contributions to fitness and adaptability. These insights, not captured by current field-standard tools, highlight how PlasAnn improves plasmid annotation and advances our understanding of plasmid biology, microbial ecology, and evolution.},
}

*Plasmids/genetics
*Molecular Sequence Annotation/methods
*Databases, Genetic
Genome, Bacterial
Software
DNA Transposable Elements
Genes, Bacterial
Bacteria/genetics

@article {pmid41588693,
year = {2026},
author = {Bhattacharya, D and Nandi, S and Chille, EE and Arroyo, M and Stephens, TG},
title = {The Host Coral Bleaching Response Viewed Through the Lens of Multi-Omics: Multi-Omics Provides the Tools to Understand the Complex Molecular Basis of Coral Bleaching, Which Can Aid Conservation Efforts.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {48},
number = {1},
pages = {e70110},
doi = {10.1002/bies.70110},
pmid = {41588693},
issn = {1521-1878},
support = {23-7825575//Catalyst Science Fund, Revive & Restore, and the National Philanthropic Trust/ ; 2128073//National Science Foundation/ ; NJ01180//USDA National Institute of Food and Agriculture Hatch Formula/ ; },
mesh = {Animals ; *Anthozoa/genetics/physiology ; Symbiosis ; *Coral Bleaching ; Genomics/methods ; Coral Reefs ; Conservation of Natural Resources ; Climate Change ; Oxidative Stress ; Heat-Shock Response ; Multiomics ; },
abstract = {We review recent multi-omics analyses of the coral heat stress response to explore the generality of the Oxidative Theory of Coral Bleaching (OTCB), which posits that algal symbiont release is the final act of defense by the coral host to survive alga-derived oxidative stress. The OTCB is particularly relevant given that ocean warming, which is accelerating under climate change, has proven devastating for corals, leading to the bleaching phenotype and widespread reef loss. Multi-omics results, in combination with other data, such as genome-wide association studies, support the idea that coral bleaching is a multifactorial response that reflects a wide array of causes and effects and is population-specific under most conditions, with coral ploidy and genotype being critical to bleaching sensitivity. This perspective leverages the location, algal and prokaryotic microbiome, and host genotype-specific aspects of coral resilience to promote a new "personal genomics" approach to coral conservation, analogous to that used in human health.},
}

Animals
*Anthozoa/genetics/physiology
Symbiosis
*Coral Bleaching
Genomics/methods
Coral Reefs
Conservation of Natural Resources
Climate Change
Oxidative Stress
Heat-Shock Response
Multiomics

@article {pmid41588622,
year = {2026},
author = {Hessl, AE and Richardson, AD and Filwett, R and Andreu-Hayles, L and Walker, M and Oelkers, R and Robison, AS and Leshyk, VO and Carbone, MS},
title = {Carbon uptake, storage, and allocation patterns contribute to blurring of annual [14]C signals in tree rings.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70868},
pmid = {41588622},
issn = {1469-8137},
support = {2411569//NSF Solar Terrestrial/ ; 2411571//NSF Solar Terrestrial/ ; 2136524//NSF GRF/ ; 1832210//NSF LTER/ ; 2224545//NSF LTER/ ; PID2021-126411OB-I00//MICIU/AEI/10.13039/501100011033/ ; },
abstract = {Tree rings are considered the gold standard for observing variation in past atmospheric radiocarbon ([14]C), yet little attention has been paid to whether different trees record tropospheric [14]C evenly. The discovery of Miyake events, rapid increases in [14]C production occurring in past millennia, has led to repeated measurements of [14]C in tree rings across species and locations. These records demonstrate remarkable synchrony, yet significant variability between samples remains, limiting reliable use of tree rings as a precise indicator of the timing and scale of past [14]C production. Understanding how trees and species record tropospheric [14]C would improve reconstructions of past [14]C production events, refine geochronological control, and because of the pulse-like nature of past [14]C production events, shed light on a fundamental question in tree physiology and dendrochronology: what is the lag time between photosynthesis, storage, and allocation to wood and how might this lag blur isotopic signals in tree rings? Here, we evaluate the implicit assumption that all trees record tropospheric [14]C evenly by focusing on the path carbon takes within trees including: phenology of carbon uptake and wood formation, storage and use of nonstructural carbohydrates, and how these factors interact to affect the tropospheric [14]C signal in wood.},
}

@article {pmid41588471,
year = {2026},
author = {Sulaiman, N and Sõukand, R and Ullah, I and Pieroni, A},
title = {Searching for a ghost?! The vain ethnobotany of foraging in three coastal Mediterranean areas.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13002-026-00853-0},
pmid = {41588471},
issn = {1746-4269},
support = {Horizon ID 101159928//ETHCSTWIN/ ; },
abstract = {This paper explores the erosion of foraging-related ethnobotanical knowledge in three coastal Mediterranean areas: Gozo Island (Malta), Kasos Island (Greece), and the Castagniccia region of Corsica Island (France). Based on recent ethnobotanical fieldwork between the summer of 2023 and the spring of 2025 in the three study areas, we document the few remaining wild vegetable uses in each region and contextualise the absence of robust LEK linked to plant foraging within broader socio-environmental changes. Our findings show that land abandonment, mass migration, desertification, and the rise of seasonal tourism have contributed to the disintegration of Local Ecological Knowledge (LEK). These forces have severed communities from everyday land-based practices, transforming vibrant ethnobotanical traditions into fragmented memories. We argue that LEK, particularly foraging knowledge, cannot survive in the absence of continuous interaction with the landscape, and that the revival of such practices requires more than nostalgic return, demanding a reconnection with local agro-ecological systems.},
}

@article {pmid41578851,
year = {2026},
author = {Peltier, DMP and Malone, SC and McIntire, CD and Thompson, RA and Pinzon-Navarro, S and Pereverzeva, KA and Richardson, AD and McDowell, NG and Adams, HD and Carbone, MS and Pockman, WT and Trowbridge, AM},
title = {Resin-based defenses in Pinus edulis are only reduced after long term drought.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag004},
pmid = {41578851},
issn = {1758-4469},
abstract = {Constrained carbon allocation towards secondary metabolites involved in chemical defense is a common explanation for widespread drought-related beetle-kill in conifers-we challenge the generality of this explanation. While monitoring drought stress (ψpd), we tracked both carbon reserves (NSC) and chemical defenses (terpenes, phenolics, resin flow) in mature Pinus edulis trees experiencing either short-term (3-year) or a "legacy" long-term (13-year) throughfall exclusion treatments, plus a control. We also quantified the Δ14C-age of resin to measure past allocation to current defense. While 72% of trees in short-term throughfall exclusion plots died (attacked by bark beetles, Ips confusus), mortality patterns were unrelated to throughfall exclusion intensity and all "legacy" trees survived. We thus assessed trees in four survivorship categories: control, "legacy", surviving, and dying trees. We found concentrations of certain defense compounds (leaf phenolics, twig monoterpenes) increased with drought stress, particularly in dying trees. In the main stem, dying trees exhibited similar terpene concentrations (94%) and phenolic concentrations (139%) relative to control trees. Compared to control trees, only "legacy" trees had reduced stem terpenes (-49%, p<0.05) after a decade of drought. Δ14C-age of resin could be up to 10.2±0.5 years old, where the oldest resin was exuded from trees with low sugar concentrations and more negative Ψpd. Our results suggest drought imposes a weak constraint on carbon allocation to resin-based defense. Instead, we primarily found evidence of increased concentrations of terpene and phenolic compounds under drought, even in dying trees, and only observed reductions in resin-based defenses after 10+ years of drought. Δ14C-ages demonstrate limited resin turnover and/or synthesis of resin from old reserves, suggesting long-term drought is required to reduce resin-based defenses. Persistent allocation coupled with past investments appears to preserve or enhance concentrations of resin-based defenses even under lethal drought stress in P. edulis.},
}

@article {pmid41578325,
year = {2026},
author = {Lim, KO and Kummerfeld, E and Anderson, LM and Wonderlich, SA and Engel, S and Crosby, RD and Peterson, CB},
title = {Personal causal modeling of affect and eating behaviors in bulimia nervosa: implications for personalized treatment.},
journal = {Journal of eating disorders},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40337-026-01524-x},
pmid = {41578325},
issn = {2050-2974},
support = {K23MH123910/NH/NIH HHS/United States ; R01MH059674/NH/NIH HHS/United States ; R34MH099040/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Affect regulation models suggest high negative and low positive affect may drive binge eating and purging in bulimia nervosa (BN). While ecological momentary assessment (EMA) studies often support these theories, inconsistent outcomes in affect-targeted interventions suggest causal relations vary across individuals. This study applied causal discovery analysis (CDA) to EMA data to characterize such heterogeneity in person-specific causal models for BN.

METHODS: EMA data from 118 adult women with BN, collected over 14 days, assessed momentary negative affect, positive affect, binge eating, and self-induced vomiting. Using the Greedy Fast Causal Inference algorithm, we derived individual causal models and estimated effect sizes via structural equation modeling. Heterogeneity was evaluated by the proportion of participants with affect as a causal factor for BN behaviors.

RESULTS: Causal patterns were highly heterogeneous. Elevated negative affect was causal for binge eating in 16.9% of participants, vomiting in 18.6%, and either behavior in 27.1%. Low positive affect was causal for binge eating in 8.5%, vomiting in 11.0%, and either behavior in 15.3%. Behavior-behavior causality was also common: vomiting caused binge eating in 26.3% of participants, and binge eating caused vomiting in 22.0%.

CONCLUSIONS: CDA revealed marked heterogeneity in causal factors underlying BN behaviors, with some models showing affect-driven behaviors and others indicating behavior-driven patterns. Ultimately, this work indicates that the link between momentary affect and BN behaviors is highly individualized, underscoring the need for precision-targeted interventions rather than one-size-fits-all treatments.},
}

@article {pmid41520592,
year = {2026},
author = {Chen, H and Liu, Y and Wang, G and Fan, W and Rong, G and Wang, H},
title = {Multi-omics and stable isotopic reveal coordinated carbon-nitrogen metabolic reprogramming sustaining diatom cellular homeostasis under CO2 limitation.},
journal = {Marine environmental research},
volume = {215},
number = {},
pages = {107843},
doi = {10.1016/j.marenvres.2026.107843},
pmid = {41520592},
issn = {1879-0291},
mesh = {*Diatoms/physiology/metabolism ; *Carbon Dioxide/metabolism ; *Nitrogen/metabolism ; *Carbon/metabolism ; Homeostasis ; Eutrophication ; Metabolomics ; Transcriptome ; Nitrogen Isotopes ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Algal blooms frequently trigger CO2 limitation, under which diatoms not only survive but dominate. However, the cellular metabolic adaptations underlying this ecological phenomenon remain poorly understood. This study systematically investigated the coordinated carbon-nitrogen metabolic response of the typical diatom Skeletonema costatum (S. costatum) to CO2 limitation (300 ppm, 100 ppm) via stable isotope and multi-omics analysis. CO2 limitation triggered the carbon concentrating mechanism (CCM) and attenuated nitrogen isotope fractionation, redirecting carbon flux towards amino acid biosynthesis rather than fatty acid biopathway. Integrated transcriptomic and metabolomic profiling revealed that carbon fixation and the tricarboxylic acid (TCA) cycle were activated, while fatty acid synthesis was inhibited. This redirected carbon skeletons from acetyl-CoA into the TCA cycle to support amino acid production. Concurrent upregulation of nitrogen assimilation genes, particularly those involved in glutamine/glutamate synthesis, facilitated ammonium incorporation. The alanine-aspartate-glutamate pathway served as a central hub, integrating carbon skeletons and amino groups to drive amino acid synthesis and maintain cellular homeostasis. These findings systematically delineate the metabolic reprogramming that enables diatoms to adapt to CO2 limitation, providing key insights into their dominance during algal blooms.},
}

*Diatoms/physiology/metabolism
*Carbon Dioxide/metabolism
*Nitrogen/metabolism
*Carbon/metabolism
Homeostasis
Eutrophication
Metabolomics
Transcriptome
Nitrogen Isotopes
Metabolic Reprogramming
Multiomics

@article {pmid41476124,
year = {2025},
author = {Abdou, ANA and Hamed, M and Hassan, AMM and Khaled, MA},
title = {Assessment of industrial pollution and water quality in the Nile River using GIS-based indices at Aswan, Egypt.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3731},
pmid = {41476124},
issn = {2045-2322},
mesh = {Egypt ; *Rivers/chemistry ; *Water Quality ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Water Pollution/analysis ; Ecosystem ; *Industrial Waste/analysis ; },
abstract = {Industrial pollution represents a critical threat to freshwater ecosystems, particularly in regions where rivers serve multiple socio-economic functions. The Nile River in Aswan Governorate, southern Egypt, is a vital source of drinking water, irrigation, fisheries, and tourism, yet it is increasingly exposed to untreated industrial effluents. This study assessed the spatial extent and intensity of such pollution using geographic information system (GIS)-based spatial interpolation alongside two comprehensive indices: the weighted arithmetic water quality index (WAWQI) and the canadian water quality index (CWQI). Findings revealed distinct pollution hotspots near major industrial discharge areas, where water quality was classified as poor to very poor (WAWQI: 52.6-127.4; CWQI: 74.2-68.3). In contrast, upstream and downstream zones more distant from effluent sources exhibited good water quality (WAWQI: 24.5-38.1; CWQI: 93.69-85.52). The most degraded sites were characterized by elevated concentrations of chemical oxygen demand (13.1-59.6 mg/L), biochemical oxygen demand (7.67-36.5 mg/L), total suspended solids (4.67-13.1 mg/L), turbidity (6.01-17.1 NTU), total nitrogen (1.13-3.35 mg/L), and phenol (8.01-10.10 µg/L). These results highlight the ecological vulnerability of the Nile River in Aswan to industrial activities, with direct implications for ecosystem health and resource sustainability. They also underscore the limitations of relying solely on traditional water quality monitoring without spatial analysis, as GIS-based interpolation proved critical in detecting pollution gradients beyond sampling sites. The study supports the enforcement of Egypt's Law 48/1982 on water protection and contributes to global sustainable development goals, particularly SDG 6 (Clean Water and Sanitation), SDG 12 (Responsible Consumption and Production), and SDG 14 (Life Below Water).},
}

Egypt
*Rivers/chemistry
*Water Quality
*Geographic Information Systems
*Environmental Monitoring/methods
*Water Pollutants, Chemical/analysis
*Water Pollution/analysis
Ecosystem
*Industrial Waste/analysis

@article {pmid41575653,
year = {2026},
author = {Astill Wright, L and Bakstein, E and Saunders, K and Guo, B and Morriss, R},
title = {Performance of active and passive ambulatory assessment measures and mood monitoring in bipolar disorder: a systematic review.},
journal = {International journal of bipolar disorders},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40345-025-00407-5},
pmid = {41575653},
issn = {2194-7511},
abstract = {BACKGROUND: Ambulatory assessment uses digital technology to capture real-time data on mood, mental state and behaviour. It has the potential to enhance traditional clinical outcome measures, but the practical application of these tools fundamentally depends on their performance.

AIMS: This systematic review aimed to assess the performance of active and passive ambulatory assessment and mood monitoring outcome measures in non-randomised and randomised studies in bipolar disorder over 3 months or longer. We aimed to evaluate their performance against established clinical measures and through inter-ambulatory assessment comparisons.

METHODS: Systematic review (PROSPERO: CRD42023396473) of performance of mood monitoring and ambulatory assessment protocols in RCTs and non-randomised studies in bipolar disorder. Identified studies were assessed for risk of bias. Due to the very high heterogeneity in included studies and performance metrics we were not able to aggregate the data via meta-analysis.

RESULTS: The review included 42 studies with a combined sample of 7,813 participants. We included 28 distinct ambulatory assessment protocols which reported 487 different smartphone-based performance metrics. The considerable variability and inconsistency across these metrics limited our ability to make definitive comparisons of performance. Overall, some active ambulatory assessment approaches showed good performance when compared with established clinical measures. There was a paucity of data examining the performance of passive ambulatory assessment measures. Most studies were rated as having low to moderate risk of bias.

CONCLUSIONS: While ambulatory assessment holds significant promise, current evidence fails to establish the validity and reliability of passive ambulatory assessment to measure mood. The substantial methodological variation-particularly in how performance metrics are defined and reported-limits meaningful comparison and replication. Greater consistency in ambulatory assessment design and reporting standards is essential to support reliable evaluation and broader adoption of these behavioural assessment tools.},
}

@article {pmid41575069,
year = {2026},
author = {Zupunski, L and Yaumenenka, A and Veyalkin, I and Minenko, V and Moiseyev, P and Schüz, J and Kukhta, T and Trofimik, S and Harbron, R and Drozdovitch, V and Ostroumova, E},
title = {Lymphoma, multiple myeloma and leukaemia incidence in regions of Belarus most heavily contaminated by the Chernobyl accident.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70346},
pmid = {41575069},
issn = {1097-0215},
abstract = {There is little information on non-thyroid cancer risks, including haematological malignancies (HM), among the residents of most contaminated regions after the Chernobyl (Chornobyl) nuclear power plant accident. We studied the incidence of lymphoma, multiple myeloma and leukaemia in relation to the raion-average age-specific cumulative absorbed red bone marrow (RBM) dose among the residents of Gomel and Mogilev oblasts in Belarus, which were highly contaminated. The follow-up period was 40 years (1978-2018). HM cases and population size data were received from the Belarusian national cancer registry and the state department of statistics. Our ecological study included 7328 lymphoma, 9476 leukaemia and 2003 multiple myeloma incident cases and 90.8 million person-years in people who were born before the accident and have attained age <80 years old. The mean (median) RBM dose accumulated by December 31, 2018 was 14.2 (6.4) mGy. We found no evidence of increased risks of Hodgkin and non-Hodgkin lymphoma, multiple myeloma or total leukaemia associated with two-year lagged raion-average cumulative RBM dose after adjustment for sex, attained age, urban/rural status and calendar period effects. There was a suggestion of an elevated relative risk of myeloid leukaemia per 100 mGy after exclusion of Gomel and Mogilev cities. Little evidence was found on interaction between selected factors, except sex, and RBM dose for each study outcome. Studies with individually reconstructed cumulative absorbed RBM doses are warranted to provide more insight on dose-effect relationships between HM risk, specifically leukaemia, and protracted environmental exposure at a low dose range.},
}

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {241},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

*Artificial Intelligence
*Metagenome/genetics
*Metagenomics/methods
Microbiota/genetics
Computational Biology/methods
Machine Learning
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid41573256,
year = {2025},
author = {Manzano-Marín, A and Böhne, A and Monteiro, R and Marcussen, T and Struck, TH and Oomen, RA and , and , and , and Howard, C and Howe, K and Blaxter, M and McCarthy, S and Wood, JMD and Martin, F and Lazar, A and Haggerty, L and Bortoluzzi, C},
title = {ERGA-BGE reference genome of Hirudo verbana, a once neglected freshwater haematophagous European medicinal leech.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {395},
pmid = {41573256},
issn = {2732-5121},
abstract = {Hirudo verbana Carena, 1820, commonly known as the southern medicinal leech, is one of several European medicinal leeches, whose full diversity has just recently started to be uncovered. Historically, it has been widely used as a medicinal leech and for centuries it was treated erroneously under the specific name of Hirudo medicinalis L. 1758. Recent molecular and taxonomic analyses have revealed subspecific diversity within the morphospecies H. verbana. Hirudo verbana is a blood-feeding species sucking blood from amphibians, fish, and mammals. It occupies freshwater habitats, typically shallow ponds and lakes. Studies show that this leech species has a "naturally limited microbiome", suggesting it may serve as a powerful model system for the study of gut microbiota. We expect this chromosome-level assembly of H. verbana to serve as a high-quality genomic resource for this most famous leech genus and to serve as a foundation to the study of the diversification and biodiversity of European medicinal leeches, as well as their gut-associated symbionts. The genome of H. verbana was assembled into two haplotypes through a phased assembly approach; however, only the primary haplotype was designated as the reference genome for annotation and downstream analyses. The entirety of the primary haplotype was assembled into 14 contiguous chromosomal pseudomolecules, including the mitogenome. This chromosome-level assembly encompasses 0.18 Gb, composed of 277 contigs and 27 scaffolds, with contig and scaffold N50 values of 1.3 Mb and 13.4 Mb, respectively.},
}

@article {pmid41566104,
year = {2026},
author = {Sau, D and Tudu, GC and Hazra, T and Shiuly, A},
title = {Evaluation of microplastic pollution in urban lentic ecosystem using remote sensing, GIS, and Support Vector Machine (SVM): relevance for environmental and ecological risk.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {2},
pages = {160},
pmid = {41566104},
issn = {1573-2959},
mesh = {*Microplastics/analysis ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Remote Sensing Technology ; India ; Support Vector Machine ; Geographic Information Systems ; Ecosystem ; Lakes/chemistry ; Risk Assessment ; },
abstract = {Plastic waste is a major source of microplastic (MP) pollution, posing adverse environmental and public health risks. This study assessed MP abundance in 24 urban ponds and lakes within the Kolkata Municipal Corporation, India, during the post- and pre-monsoon seasons of 2022-2023. Results showed that MP concentrations were significantly higher in the post-monsoon season (20 ± 3.46 items L[-][1]; ANOVA, p < 0.05), with red, white, and black particles being the most prevalent. MPs prevalently ranged between 500 and 1000 µm with fibers constituting 58-59% of the total MPs. Fourier-transform infrared (FTIR) analysis identified polyethylene (PE) as the dominant polymer. MP abundance showed negative correlations with dissolved oxygen and turbidity, and positive associations with pH, TDS, BOD5, and total coliform counts. A Support Vector Machine (SVM) model was developed for morphology-based MP classification, achieving an accuracy of 89%. Additionally, remote sensing and GIS techniques were used to develop index-based models for water-body identification and MP quantification (items L[-][1]) using spectral data from Sentinel-2 imagery. These models demonstrated high validation accuracy of 98.01% and 92.60%, respectively. Metal analysis of sediment and MPs of water detected chromium, suggesting possible MP-metal interactions within sediments. Although the Pollution Load Index (PLI) indicated relatively low contamination levels, the Polymer Hazard Index (PHI) exceeded 1000, indicating substantial ecological risk. Future studies should focus on long-term monitoring, socio-economic and health impact assessments and development of effective mitigation strategies particularly addressing plastic-waste derived-MPS.},
}

*Microplastics/analysis
*Environmental Monitoring/methods
*Water Pollutants, Chemical/analysis
Remote Sensing Technology
India
Support Vector Machine
Geographic Information Systems
Ecosystem
Lakes/chemistry
Risk Assessment

@article {pmid41561390,
year = {2026},
author = {Fehrenbach, A and Mitrofanov, A and Backofen, R and Baumdicker, F},
title = {The complexity of multiple CRISPR arrays in strains with (co-occurring) CRISPR systems.},
journal = {microLife},
volume = {7},
number = {},
pages = {uqaf042},
pmid = {41561390},
issn = {2633-6693},
abstract = {CRISPR and their associated Cas proteins provide adaptive immunity in prokaryotes, protecting against invading genetic elements. These systems are categorized into types and are highly diverse. Genomes often harbor multiple CRISPR arrays varying in length and distance from Cas loci. However, the ecological roles of multiple CRISPR arrays and their interactions with multiple Cas loci remain poorly understood. We present a comprehensive analysis of CRISPR systems that uncovers variation between diverse Cas types regarding the occurrence of multiple arrays, the distribution of their lengths and positions relative to Cas loci, and the diversity of their repeat sequences. Some types tend to occur as the sole Cas locus present in the genome, but typically have two or more associated arrays, especially for types I-E and I-F. Multiple Cas types are also common, with some systems showing a preference for specific co-occurrence. Distinct array distributions and orientations around Cas loci indicate substantial differences in functionality and transcriptional behavior among Cas types. Our analysis suggests that arrays with identical repeats in the same genome acquire new spacers at comparable rates, irrespective of their proximity to the Cas locus. Furthermore, repeat similarities indicate that arrays of systems that often co-occur with other systems tend to have more diverse repeats than those mostly appearing alongside solitary systems. Our results indicate that co-occurring Cas-type pairs might not only collaborate in spacer acquisition but also maintain independent and complementary functions and that CRISPR systems distribute their defensive spacer repertoire equally across multiple CRISPR arrays.},
}

@article {pmid41559958,
year = {2026},
author = {Lin, Y and Liu, Y and Tan, Y and Wu, N and Wang, L and Chen, J and Sun, X and Dong, X and Chen, B and Pan, Z and Wang, W and Lin, C},
title = {Source apportionment and ecological risks of trace metals in multiple media in a typical Chinese industrialized bay on the basis of SOM, PMF and GIS methods.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119039},
doi = {10.1016/j.marpolbul.2025.119039},
pmid = {41559958},
issn = {1879-3363},
mesh = {*Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; China ; Bays/chemistry ; Geologic Sediments/chemistry ; Geographic Information Systems ; Seawater/chemistry ; *Trace Elements/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; },
abstract = {The concentrations and risks of trace metals (TMs) in different media of aquatic systems are gradually increasing, driven by increasingly frequent anthropogenic activities. This research aimed to examine the distribution and bioaccumulation patterns of TMs in various environmental media via the analysis of samples from a typical petrochemical industrial bay in southern China. In addition, the ecological risks and anthropogenic sources of these elements were assessed. The results indicated that the levels of Zn and Hg were highest and lowest, respectively, in surface seawater, sediment, and seafood, with other TMs varying in content between those of these two trace metals. The integrated pollution index (IPI) values for TMs in seawater ranged from 1.13 to 3.16, remaining at a minimal contamination level. After multiple pollution assessment methods, were comprehensively applied, Cd and Hg were highlighted as key contributors to significant pollutant buildup and elevated ecological risks in sediments. Based on the combined use of geographic information system (GIS), self-organizing map (SOM), and positive matrix factorization (PMF) methods, the sources and contributions of TMs were analysed. The results revealed that fossil fuel combustion (24.3 %), natural geological processes (48.0 %), and aquaculture practices (27.7 %) were the primary sources of TM accumulation in sediments. This study provides important data for reducing TM pollution in typical petrochemical industry bays, enhancing ecological safety, and assessing the risks of potentially toxic elements in seafood to human health.},
}

*Environmental Monitoring/methods
*Water Pollutants, Chemical/analysis
China
Bays/chemistry
Geologic Sediments/chemistry
Geographic Information Systems
Seawater/chemistry
*Trace Elements/analysis
Risk Assessment
*Metals, Heavy/analysis

@article {pmid41547987,
year = {2026},
author = {Ding, S and Zhou, F and Yang, S and Li, Y and Ma, Y and Qiu, Y},
title = {Chromosome-level genome assembly of a Chinese evergreen sweetgum (Liquidambar gracilipes, Altingiaceae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {66},
pmid = {41547987},
issn = {2052-4463},
support = {32300202//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {China ; *Chromosomes, Plant ; *Genome, Plant ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Liquidambar gracilipes, an evergreen species endemic to China and a member of the Altingiaceae family, is morphologically distinguished by its unlobed leaves and represents an ecologically and economically valuable resource. Prized for its ornamental beauty, valuable timber, and medicinal properties, this species is a key component of subtropical evergreen broad-leaved forests in East China. To improve our understanding of its evolutionary and functional genomics, we performed a de novo genome assembly of L. gracilipes by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C data. A high-quality chromosome-level genome assembly was obtained with a genome size of approximately 715.54 Mb and contig N50 of 18.61 Mb, of which 96.87% was anchored to 16 pseudo-chromosomes with a scaffold N50 of 42.40 Mb. Genome annotation identified 24,809 protein-coding genes (97.02% functionally annotated) and revealed a repetitive sequence content of 59.72%. BUSCO analysis against the embryophyte dataset indicated a high level of completeness, with a score of 98.70%. The high-quality genome assembly of L. gracilipes provides a valuable genetic resource for molecular breeding of sweetgums and lays the foundation for future in-depth evolutionary and functional genomics studies of this species.},
}

China
*Chromosomes, Plant
*Genome, Plant
Molecular Sequence Annotation
Datasets as Topic

@article {pmid41529073,
year = {2026},
author = {Vessman, B and Guridi-Fernández, P and Arias-Sánchez, FI and Mitri, S},
title = {Novel artificial selection method improves function of simulated microbial communities.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013863},
doi = {10.1371/journal.pcbi.1013863},
pmid = {41529073},
issn = {1553-7358},
mesh = {Computer Simulation ; *Microbiota/physiology/genetics ; Computational Biology ; *Models, Biological ; *Selection, Genetic ; },
abstract = {There is increasing interest in artificially selecting or breeding microbial communities, but experiments have reported modest success. Here, we develop computational models to simulate two previously known selection methods and compare them to a new "disassembly" method. We evaluate all three methods in their ability to find a community that could efficiently degrade toxins, whereby investment into degradation results in slower growth. Our disassembly method relies on repeatedly competing different communities of known species combinations against one another, while regularly shuffling around their species combinations. This approach allows many species combinations to be explored, thereby maintaining enough between-community diversity for selection to act on, and resulting in communities with high performance. Nevertheless, selection at the community level in our simulations did not counteract selection at the individual level, nor the communities' ecological dynamics. Species in our model evolved to invest less into community function and more into growth, but increased growth compensated for reduced investment, such that overall community performance was barely affected by within-species evolution. Within-community ecological dynamics were more of a challenge, as we could control them during the selection process, but community composition and function dropped in the longer term. Our work shows that the strength of disassembly lies mainly in its ability to explore different species combinations, and helps to propose alternative designs for community selection experiments.},
}

Computer Simulation
*Microbiota/physiology/genetics
Computational Biology
*Models, Biological
*Selection, Genetic

@article {pmid41482560,
year = {2026},
author = {Chakaroun, RM and Pradhan, M and Björnson, E and Arvidsson, D and Fridolfsson, J and Gummesson, A and Schoeler, M and Mitteregger, M and Smith, GJ and Larsson, I and Börjesson, M and Blüher, M and Uhlén, M and Stumvoll, M and Bergström, G and Tremaroli, V and Bäckhed, F},
title = {Multi-omic definition of metabolic obesity through adipose tissue-microbiome interactions.},
journal = {Nature medicine},
volume = {32},
number = {1},
pages = {113-125},
pmid = {41482560},
issn = {1546-170X},
support = {2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0026//Diabetesfonden (Stiftelsen Svenska Diabetesförbundets Forskningsfond)/ ; 20210366//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20240882//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF15OC0016798//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21OC0070298//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24OC0092455//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 17CVD01//Fondation Leducq/ ; ERC-2022-ADG 101096705//Fondation Leducq/ ; 2019-01599//Vetenskapsrådet (Swedish Research Council)/ ; EXC3105/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Obesity/metabolism/microbiology ; *Adipose Tissue/metabolism/microbiology ; Male ; Body Mass Index ; Female ; Middle Aged ; *Microbiota/physiology ; Adult ; Metabolome ; Insulin Resistance ; Metabolomics/methods ; Adiposity ; Multiomics ; },
abstract = {Obesity's metabolic heterogeneity is not fully captured by body mass index (BMI). Here we show that deep multi-omics phenotyping of 1,408 individuals defines a metabolome-informed obesity metric (metBMI) that captures adipose tissue-related dysfunction across organ systems. In an external cohort (n = 466), metBMI explained 52% of BMI variance and more accurately reflected adiposity than other omics models. Individuals with higher-than-expected metBMI had 2-5-fold higher odds of fatty liver disease, diabetes, severe visceral fat accumulation and attenuation, insulin resistance, hyperinsulinemia and inflammation and, in bariatric surgery (n = 75), achieved 30% less weight loss. This obesogenic signature aligned with reduced microbiome richness, altered ecology and functional potential. A 66-metabolite panel retained 38.6% explanatory power, with 90% covarying with the microbiome. Mediation analysis revealed a bidirectional, metabolite-centered host-microbiome axis, mediated by lipids, amino acids and diet-derived metabolites. These findings define an adipose-linked, microbiome-connected metabolic signature that outperforms BMI in stratifying cardiometabolic risk and guiding precision interventions.},
}

Humans
*Obesity/metabolism/microbiology
*Adipose Tissue/metabolism/microbiology
Male
Body Mass Index
Female
Middle Aged
*Microbiota/physiology
Adult
Metabolome
Insulin Resistance
Metabolomics/methods
Adiposity
Multiomics

@article {pmid41475601,
year = {2026},
author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W},
title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133911},
doi = {10.1016/j.biortech.2025.133911},
pmid = {41475601},
issn = {1873-2976},
mesh = {*Wastewater/microbiology ; *Bacteria/genetics/metabolism ; *Food Handling ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/metabolism ; *Yeasts/genetics/metabolism ; *Food-Processing Industry ; Multiomics ; },
abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.},
}

*Wastewater/microbiology
*Bacteria/genetics/metabolism
*Food Handling
Metagenomics
RNA, Ribosomal, 16S/genetics
*Fungi/genetics/metabolism
*Yeasts/genetics/metabolism
*Food-Processing Industry
Multiomics

@article {pmid41456016,
year = {2025},
author = {Guo, W and Chen, Y and Fan, H and Huang, X and Chen, X and Xiao, Y and Zhang, C and Zhou, W and Wei, F},
title = {Pygmy sperm whale multi-omics data reveal hypoxia adaptations in deep-diving cetaceans.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {20},
pmid = {41456016},
issn = {1741-7007},
mesh = {Animals ; *Adaptation, Physiological/genetics ; *Hypoxia/genetics ; Genome ; *Whales/physiology/genetics ; Multiomics ; },
abstract = {BACKGROUND: Deep-diving cetaceans tolerate acute hypoxia better than their terrestrial ancestors and shallow-diving counterparts. However, our poor understanding of how genetic factors, cellular functions, and physiological characteristics combine to drive hypoxia adaptation in deep-diving cetaceans remains a critical gap.

RESULTS: Here, we studied the genetic basis for this ability by creating a de novo genome assembly for the pygmy sperm whale (Kogia breviceps) and comparatively analyzing genomes from 12 cetacean species, including 2 other deep-diving cetaceans. We also sequenced and compared single-nucleus RNA data from the muscle and heart of the pygmy sperm whale and its terrestrial relative Bos taurus. We found that genetic and cellular changes in the HIF-1 pathway, electron transport chain, glucose and fatty acid catabolism, and heart rate may contribute to hypoxia tolerance in deep-diving cetaceans. Key adaptations include rapid evolution of glycolysis-related genes (PYGM and ENO3), differential expression of HIF-1 pathway genes like ARNT, and accelerated conserved noncoding elements in genes such as ATP5F1E (ATP synthase) and DMD (dystrophin). We found an increase in myocytes and type II cardiomyocytes in the pygmy sperm whale's muscle and heart tissues, which may support energy metabolism and homeostasis during deep dives.

CONCLUSIONS: These findings suggest deep-diving cetaceans have unique genetic and cellular adaptations to cope with hypoxia, offering insights into how mammals handle low oxygen levels at the cellular level.},
}

Animals
*Adaptation, Physiological/genetics
*Hypoxia/genetics
Genome
*Whales/physiology/genetics
Multiomics

@article {pmid41559770,
year = {2026},
author = {Novak, M and Foust, P and Hennessey, S and Tanis, BP and Coblentz, KE and Wolf, C and Segui, LM and Henderson, JS and Ingeman, KE and Falke, LP and Layden, TJ and Gradison, DJ and Randell, Z and Harris, CL and Lester, S and Naito, KA and Nakata, T and Nichols, G and Postma, BC and Alves, R and Jarman, CN and Kalytiak-Davis, AR and Martin, A and Pajiah, TJ and Pinos-Sánchez, A and Preston, DL},
title = {FracFeed: Global database of the fraction of feeding predators.},
journal = {Ecology},
volume = {107},
number = {1},
pages = {e70296},
doi = {10.1002/ecy.70296},
pmid = {41559770},
issn = {1939-9170},
support = {DEB-1353827//Division of Environmental Biology/ ; },
mesh = {Animals ; *Predatory Behavior/physiology ; *Databases, Factual ; *Feeding Behavior/physiology ; *Diet ; *Vertebrates/physiology ; *Food Chain ; *Invertebrates/physiology ; Gastrointestinal Contents ; },
abstract = {The proportion of individuals that are found to have empty stomachs during a survey of a predator population's diet has been used as an indicator of the average individual's state of energy balance and of the degree to which its feeding rate (i.e., its functional response) is saturated with respect to prey availability. As such, the proportion of empty stomachs provides insights into the effects of prey on predators and vice versa, although it is typically unreported in deference to descriptions of the contents of the non-empty stomachs. The FracFeed database is an ongoing compilation of the proportions of empty and non-empty stomachs (for gut content surveys) and of feeding and not feeding individuals (for direct observation surveys) reported in publications of predator diet surveys. FracFeed contains data from 4920 diet surveys on 1507 taxa (>4.3 million individuals) spanning cnidarians, ctenophores, chaetognaths, birds, annelids, amphibians, arthropods, mammals, mollusks, reptiles, echinoderms, and fishes that were surveyed in terrestrial, marine, and freshwater ecosystems across the globe over more than 135 years (1887-2023). For most surveys, covariate data include information on the spatial and temporal extent of the diet survey, its central geographical coordinates, the method by which the survey was performed (lethal gut contents, lavage, or direct observation), as well as each predator's standardized taxonomic name and identifier in the Open Tree of Life, its body mass (compiled mostly from independent compilations and additional publications), and its apparent diet's taxonomic richness and resolution. We appeal to more researchers who perform diet surveys to report on the number of empty stomachs they find and encourage additional contributions to the database-particularly from underrepresented geographic regions (e.g., North and Central Asia, North and Central Africa)-to help grow its scope and utility. The database is provided under a CC-BY-NC-S4 4.0 license. Users are requested to cite this data paper when using the data.},
}

Animals
*Predatory Behavior/physiology
*Databases, Factual
*Feeding Behavior/physiology
*Diet
*Vertebrates/physiology
*Food Chain
*Invertebrates/physiology
Gastrointestinal Contents

@article {pmid41559348,
year = {2026},
author = {Deng, Y and Li, J and Wang, P and Luo, X and Xu, H and Xiao, Y and Wang, Z and Lu, Y and Chen, Y and Ge, F},
title = {DNAJB6 as an immuno-oncogenic hub in liver hepatocellular carcinoma: multi-omic profiling reveals prognostic significance and therapeutic vulnerability.},
journal = {Journal of molecular histology},
volume = {57},
number = {1},
pages = {57},
pmid = {41559348},
issn = {1567-2387},
support = {31601036//National Natural Science Foundation of China/ ; 32261133523//National Natural Science Foundation of China/ ; B2023023//Scientific Research Plan Project of Hubei Provincial Department of Education/ ; },
mesh = {Humans ; *Liver Neoplasms/genetics/immunology/pathology/metabolism ; *Carcinoma, Hepatocellular/genetics/immunology/pathology/metabolism ; *HSP40 Heat-Shock Proteins/genetics/metabolism ; Prognosis ; *Molecular Chaperones/genetics/metabolism ; Hep G2 Cells ; *Nerve Tissue Proteins/genetics/metabolism ; Gene Expression Regulation, Neoplastic ; Male ; Female ; Apoptosis/genetics ; Cell Proliferation ; Biomarkers, Tumor ; Middle Aged ; Gene Expression Profiling ; Multiomics ; },
abstract = {The DnaJ/Hsp40 family member B6 (DNAJB6) is a protein aggregation inhibitor, and its dysregulation has been associated with various diseases. Although early studies implicated DNAJB6's role in tumor progression, its prognostic and immunotherapy predictive value across cancers remain undefined. Integrated multi-omics data analysis revealed significant upregulation of DNAJB6 in multiple tumors, particularly in liver hepatocellular carcinoma (LIHC), supported by immunohistochemistry of liver tumor tissues and Western blot assays in HepG2 cells, and poor prognosis in LIHC patients was linked to increased DNAJB6 expression. ROC and univariate Cox analyses established DNAJB6 as an independent prognostic factor in LIHC, with good predictive value. Enrichment, immune scoring and single-cell sequencing analyses indicated that DNAJB6 was linked to immune responses, especially with myeloid-derived suppressor cell (MDSC) and exhausted CD8[+] T cell (Tex). Cell experiments demonstrated that siRNA targeting DNAJB6 inhibited HepG2 cells from proliferating and migrating while inducing apoptosis. Furthermore, we predicted and experimentally confirmed that DNAJB6 silencing conferred gefitinib resistance in HepG2 cells. In conclusion, our findings highlighted the significance of DNAJB6 expression in determining LIHC prognosis and immunotherapy response, as well as its potential in developing novel anti-cancer drugs and enhancing immunotherapy.},
}

Humans
*Liver Neoplasms/genetics/immunology/pathology/metabolism
*Carcinoma, Hepatocellular/genetics/immunology/pathology/metabolism
*HSP40 Heat-Shock Proteins/genetics/metabolism
Prognosis
*Molecular Chaperones/genetics/metabolism
Hep G2 Cells
*Nerve Tissue Proteins/genetics/metabolism
Gene Expression Regulation, Neoplastic
Male
Female
Apoptosis/genetics
Cell Proliferation
Biomarkers, Tumor
Middle Aged
Gene Expression Profiling
Multiomics

@article {pmid41557733,
year = {2026},
author = {Smith, C and Kasoar, M and Perkins, O and Millington, JDA and Mistry, J},
title = {Small-scale livelihood and cultural fire: Global spatiotemporal characteristics, and gaps in data.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339561},
doi = {10.1371/journal.pone.0339561},
pmid = {41557733},
issn = {1932-6203},
mesh = {Humans ; *Fires ; Ecosystem ; Spatio-Temporal Analysis ; Databases, Factual ; *Conservation of Natural Resources ; Agriculture ; *Wildfires ; },
abstract = {Human fire use is a key activity and process in many landscapes and ecosystems around the world, varying spatiotemporally depending on social, economic, and ecological factors. Recently, initiatives have begun to synthesise data on global fire use from across multiple disciplines and disparate sources into coherent databases. Here, we draw on information from one of these databases, the Livelihood Fire Database, which collates data on fire use practices worldwide from case studies in the literature. We examine data from 345 case study locations spanning 69 countries regarding return interval, area burned, and seasonality of anthropogenic fires set to meet small-scale rural livelihood objectives and/or for cultural reasons. We distinguish patterns in the spatiotemporal nature of fires associated with different fire-use purposes, such as clearing vegetation for agriculture, maintaining pasture for livestock, promoting certain plant species for gathering, or driving game when hunting. For many fire uses, especially those related to hunting, gathering, human wellbeing, and social signalling, there are very limited quantitative data available, but it is possible to draw qualitative insights from case studies. Case studies demonstrate that environmental and social conditions drive variation in fire use for the same purpose, reiterating that assumptions of uniform drivers of anthropogenic fire may be misleading. Nonetheless where quantitative data are available, we find some correspondence between the spatiotemporal nature of fires and fire-use purpose, suggesting that distinguishing between different fire-use purposes may be useful to understand and to better model their likely timing, size, and frequency relative to climate and other drivers. We recommend examples where the diagnosis of these broad relationships between fire-use purpose and fire properties could enable improved representation of anthropogenic fire in global land surface models, and aid interpretation of remote sensing data. Many of the smaller fires now being revealed in global burned area data by new fine-scale remote sensing products are likely human-set; continued collection, collation, and analyses of case study data on human fire use globally will be essential to help interpret this improved detection of small fires, and to ensure appropriate representation of the underlying drivers of human activity when modelling fire regimes.},
}

Humans
*Fires
Ecosystem
Spatio-Temporal Analysis
Databases, Factual
*Conservation of Natural Resources
Agriculture
*Wildfires

@article {pmid41442946,
year = {2026},
author = {Huang, XL and Xiong, YX and Yu, S and Chen, XW and Li, DW and Ou, LJ},
title = {Construction of a coccolithophore database platform for ecological and molecular applications.},
journal = {Water research},
volume = {291},
number = {},
pages = {125107},
doi = {10.1016/j.watres.2025.125107},
pmid = {41442946},
issn = {1879-2448},
mesh = {*Haptophyta/genetics ; *Databases, Factual ; China ; Microalgae ; },
abstract = {Coccolithophores play a critical role in marine carbon cycling and biogeochemical processes, yet their ecological distribution and in situ abundance remain understood. This study introduces an open-access coccolithophore database, integrating global occurrence records of Gephyrocapsa huxleyi and Chrysotila spp. from multiple microalgal datasets. The platform integrates taxonomic, distributional, and ecological information of coccolithophores, offering BLAST-based sequence analysis and user data submission features to enhance ecological monitoring and functional studies. To evaluate the database's utility and quantify field abundance, we developed and validated species-specific qPCR primers, demonstrating high specificity and efficiency. Application in Daya Bay, China, revealed G. huxleyi as dominant in offshore and central regions, while C. dentata showed lower abundance, confined to nearshore areas. QPCR-based estimates aligned closely with microscopy-based counts (R[2] > 0.89), affirming method reliability. This study provides a robust digital framework and molecular tools, advancing systematic monitoring of coccolithophore communities and their contributions to oceanic carbon cycling.},
}

*Haptophyta/genetics
*Databases, Factual
China
Microalgae

@article {pmid41556837,
year = {2026},
author = {McConnell, RD and Jarrett, C and Ferreira, DF and Powell, LL and Quiñones, ALS and Dominoni, DM and Welch, AJ},
title = {Dietary DNA Metabarcoding From Animal Fecal Samples.},
journal = {Current protocols},
volume = {6},
number = {1},
pages = {e70226},
doi = {10.1002/cpz1.70226},
pmid = {41556837},
issn = {2691-1299},
mesh = {*Feces/chemistry ; Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA/genetics ; *Diet ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; },
abstract = {Fecal DNA metabarcoding is a powerful tool for examining animal diets with unprecedented resolution, offering insights into ecological patterns shaped by trophic interactions. As a result, dietary metabarcoding has become widely applied across ecology, evolution, behavior, and conservation. This article provides a practical guide to the key steps involved in metabarcoding animal fecal samples, from field collection and storage through to laboratory processes, such as DNA extraction, PCR amplification, and sequencing library preparation. It also outlines a bioinformatics workflow using the open-source QIIME2 platform to filter, error-correct, and assign taxonomy to dietary DNA sequences. We present key considerations for study design, highlighting potential caveats and limitations to enable researchers to make informed methodological choices. In addition, we offer guidance on the statistical analysis of diet data, including generalized linear models, multivariate analyses, and network analyses. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metabarcoding library preparation of animal fecal dietary DNA for Illumina MiSeq sequencing Support Protocol 1: Making a SpeedBeads solution Support Protocol 2: Calibrating the SpeedBeads solution Basic Protocol 2: QIIME2 bioinformatics workflow for metabarcoded dietary DNA.},
}

*Feces/chemistry
Animals
*DNA Barcoding, Taxonomic/methods
*DNA/genetics
*Diet
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods

@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}

*Metagenomics/methods
*Software
Workflow
*Computational Biology/methods
Microbiota

@article {pmid41550274,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Barred Straw, Gandaritis pyraliata (Denis & Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {435},
doi = {10.12688/wellcomeopenres.19526.2},
pmid = {41550274},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Gandaritis pyraliata (the Barred Straw; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 295.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.74 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,805 protein coding genes.},
}

@article {pmid41550075,
year = {2026},
author = {Patron-Rivero, C and Yañez-Arenas, C and Ruane, S and Chiappa-Carrara, X and Rojas-Soto, OR},
title = {A comprehensive morphological database of hognose Porthidium pitvipers (Viperidae: Crotalinae).},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
doi = {10.1093/database/baaf085},
pmid = {41550075},
issn = {1758-0463},
support = {1010703//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; //Programa de Apoyo a los Estudios de Posgrado/ ; //Secretaría de Investigación, Innovación y Educación Superior/ ; },
mesh = {Animals ; *Viperidae/anatomy & histology/classification ; *Databases, Factual ; },
abstract = {Generating and sharing primary biological data is essential to support reproducible research, stimulate new hypotheses, and advance our understanding of biodiversity. Here, we present a comprehensive database of morphological traits for snakes of the genus Porthidium (Viperidae: Crotalinae). This database includes linear measurements, pholidosis (scale counts), and head shape data from preserved specimens across five different herpetological collections. These data comprise 13 morphological traits, 8 scale counts, and 55 landmarks collected from 484 individuals across 9 species. The specimens represent both juvenile and adult stages. All data were collected using standardized protocols to ensure comparability across individuals and species. The dataset is a valuable resource for studies in systematics, morphological evolution, ecological adaptation, and ontogeny, as well as facilitating reproducibility and reuse in the fields of evolutionary biology, herpetology, and comparative morphology.},
}

Animals
*Viperidae/anatomy & histology/classification
*Databases, Factual

@article {pmid41548666,
year = {2026},
author = {van Kessel, SAM and Schoffelen, AF and van Son, KHS and Notermans, DW and Severin, JA and Bakhshi-Raiez, F and Velthuis, F and Schipper, M and Dongelmans, D and Verbon, A and Wielders, CCH and , and , },
title = {Water-free care in Dutch ICU patient rooms: impact on gram-negative bacteria detections in routine patient care.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.12.013},
pmid = {41548666},
issn = {1532-2939},
abstract = {BACKGROUND: Patients in intensive care units (ICUs) are at increased risk of healthcare-associated infections with gram-negative bacteria (GNB), for which sinks in patient rooms are known reservoirs. We investigated the association between water-free care practices and the incidence of GNB detections in Dutch ICUs in non-outbreak settings.

METHODS: We performed a retrospective ecological study (2018-2022) using data from the Infectious diseases Surveillance Information System-Antibiotic Resistance (ISIS-AR), the National Intensive Care Evaluation registry, and a questionnaire on water-free care. Detections (colonisation and infections) of seven bacteria groups (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter spp., all Enterobacterales, extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E), carbapenemase-producing Enterobacterales) were analysed at ICU-year level. Incidence rate ratios (IRRs) were calculated for water-free vs. non-water-free ICUs, adjusted for ICU and patient characteristics.

FINDINGS: Data from 37 ICUs were analysed, 22 ICU-years in the water-free and 131 in the non-water-free group. Water-free ICUs were larger, with more surgery admissions and mechanically ventilated patients. For all bacteria, adjusted IRRs were close to 1 with broad 95%CIs, ranging from 0.82 (95%CI 0.44-1.52) for ESBL-E to 1.39 (95%CI 0.69-2.84) for Acinetobacter spp. Sensitivity analyses showed similar results.

CONCLUSION: Although positive effects of water-free care on GNB detection rates have been described in single ICUs, these findings were not reflected in this Dutch multi-centre study. Possible explanations are low infection prevalences, high prevention standards, widespread usage of selective decontamination, and insufficient power to detect small differences. Evidence for benefits of water-free care in non-outbreak settings remains limited, highlighting the importance of future research in different ICU settings.},
}

@article {pmid41546619,
year = {2026},
author = {Atighi, MR and Meijer, A and De Meyer, T and Vandepoele, K and Kyndt, T},
title = {Ready for battle: histone modifications shape rice intergenerational memory to protect against nematode attack.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag020},
pmid = {41546619},
issn = {1460-2431},
abstract = {Accumulating scientific insights reveal the ecological and evolutionary implications of phenotypic plant plasticity in response to biotic and abiotic stress factors. This study confirms that root-knot nematode infection leads to intergenerational acquired resistance (IAR) in rice offspring. Genome-wide and targeted gene expression analyses demonstrated that offspring of nematode-infected rice plants are better prepared to fight against such attack through 'spring loading' of hormone-related plant defense genes. These genes are suppressed under basal conditions in IAR plants but show a more dramatic induction upon nematode attack. Here, ChIP-sequencing was executed on the offspring of IAR versus naive plants to investigate if histone modifications could be involved in the spring-loaded expression pattern. This revealed enrichment of H3K4me3 on defence related genes and H3K27me3 on development-related genes in roots of IAR plants. Detailed bio-informatic analyses pointed towards significant epigenetic changes to the ABA, ET and MAPK signalling pathways in the offspring of nematode-infected plants. A rice line with reduced activity for OsMPK5 was found to be deficient in defense spring loading and the IAR phenotype. Transmitting a memory of encountered stress factors to one's offspring is arguably an important asset for the adaptation of sessile plant communities to hostile environments.},
}

@article {pmid41385957,
year = {2026},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
pmid = {41385957},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; },
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}

Animals
*Ducks/microbiology/physiology
*Gastrointestinal Microbiome
Domestication
*Adaptation, Physiological
Cecum/microbiology
Ileum/microbiology
*Metabolome
Metabolomics
Multiomics

@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}

*Fermentation
*Moringa oleifera/microbiology/chemistry
*Taste
*Plant Leaves/microbiology/chemistry
Gas Chromatography-Mass Spectrometry
Volatile Organic Compounds/analysis
Odorants/analysis
Amino Acids/analysis
*Food Microbiology
Flavoring Agents
*Fermented Foods/microbiology
Bacteria/metabolism/classification/genetics
Microbiota
Metagenomics
Multiomics

@article {pmid41539503,
year = {2026},
author = {Li, S and Liu, J and Li, J and Han, M and Zhang, X and Wu, Z and Hu, S and Jin, H and Hua, K and Tu, K},
title = {Eco-friendly chitosan-based hydrogel for coal dust suppression via salting-out effect.},
journal = {International journal of biological macromolecules},
volume = {341},
number = {Pt 1},
pages = {150171},
doi = {10.1016/j.ijbiomac.2026.150171},
pmid = {41539503},
issn = {1879-0003},
abstract = {Coal mining-related dust pollution poses significant threats to ecological integrity, occupational health, and industrial sustainability. Conventional dust suppressants, however, suffer from inherent limitations such as inadequate capture efficiency, poor water retention, and a tendency to cause secondary pollution. To overcome these challenges, this study developed a novel bio-based chitosan hydrogel dust suppressant using highly deacetylated chitosan and sodium citrate via an innovative salting-out method. By acting as both a salting-out agent and a pH regulator, sodium citrate enhances the binding affinity with coal dust to improve suppression performance. Its dust suppression primarily occurs through synergistic mechanisms including electrostatic adsorption, moisture retention/locking, and physical coverage. After 72 h, the hydrogel dust suppressant maintained a water retention rate close to 75%. Its wind erosion resistance rate remained at approximately 99% within 3-7 days, and its degradation rate reached about 96% within 25 days. Notably, compared to conventional materials, this formulation exhibits excellent biodegradability, with its carbon-containing degradation products providing nutrients for plant growth. This green multifunctional system avoids complex preparation processes, integrating high-efficiency dust suppression, environmental safety, and ecological compatibility. It demonstrates significant application potential in sustainable mining practices.},
}

@article {pmid41404704,
year = {2026},
author = {Saghaei, S and Siemers, M and Ossetek, KL and Richter, S and Edwards, RA and Roux, S and Zielezinski, A and Dutilh, BE and Marz, M and Cassman, NA},
title = {VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D912-D924},
pmid = {41404704},
issn = {1362-4962},
support = {//NFDI4Microbiota/ ; 460129525//Deutsche Forschungemeinschaft/ ; ZMII2-2524FSB62C//German Federal Ministry of Health/ ; 390713860//Germany's Excellence Strategy EXC 2051/ ; 101046203//Horizon Europe programme/ ; //PHI/ ; //Alexander von Humboldt Foundation/ ; //Federal Ministry of Education and Research/ ; DP220102915//Australian Research Council/ ; DP250103825//Australian Research Council/ ; FL250100019//Australian Research Council/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; //Friedrich-Schiller-Universität Jena/ ; 865694/ERC_/European Research Council/International ; },
mesh = {*Viruses/genetics/classification ; *Software ; *Computational Biology/methods ; Metadata ; Internet ; High-Throughput Nucleotide Sequencing ; *Databases, Genetic ; Data Curation ; Genome, Viral ; },
abstract = {High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.},
}

*Viruses/genetics/classification
*Software
*Computational Biology/methods
Metadata
Internet
High-Throughput Nucleotide Sequencing
*Databases, Genetic
Data Curation
Genome, Viral

@article {pmid41316726,
year = {2026},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D902-D911},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}

*Genome, Viral
*Virome/genetics
*Metagenome
*Viruses/genetics/classification
*Databases, Genetic
Metagenomics/methods
Open Reading Frames
Microbiota/genetics
Humans
Software
Molecular Sequence Annotation

@article {pmid41312645,
year = {2026},
author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC},
title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D801-D812},
pmid = {41312645},
issn = {1362-4962},
support = {DE-AC02-05CH11231//US DOE/ ; FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Hellenic Foundation for Research and Innovation/ ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; },
mesh = {*Genome, Viral ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Phylogeny ; Biodiversity ; Genetic Variation ; Metagenome ; Software ; },
abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.},
}

*Genome, Viral
*Viruses/genetics/classification
*Databases, Genetic
Metagenomics/methods
Phylogeny
Biodiversity
Genetic Variation
Metagenome
Software

@article {pmid41263111,
year = {2026},
author = {Feng, X and Li, Y and Zheng, J and Chen, X and Yang, S and Chen, Y and Li, SC},
title = {MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D842-D851},
pmid = {41263111},
issn = {1362-4962},
support = {C2004-23Y//Young Collaborative Research/ ; JCYJ20220818101201004//Shenzhen Science and Technology Program/ ; 32300527//National Natural Science Foundation of China/ ; 32470695//National Natural Science Foundation of China/ ; 2022A1515110784//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303040004//Key-Area Research and Development Program of Guangdong Province/ ; TC2024JC43//Basic Research Programs of Taicang, 2024/ ; //Shenzhen-Hong Kong Institute of Brain Science/ ; //SIAT-HKUST Joint Laboratory of Brain Science/ ; },
mesh = {*Molecular Sequence Annotation ; Archaea/genetics ; *Databases, Genetic ; Fungi/genetics ; Genome, Viral ; Genome, Archaeal ; Bacteria/genetics ; Viruses/genetics ; *Genomics/methods ; *Software ; Genome, Fungal ; Genome, Bacterial ; Computational Biology/methods ; Metagenome ; },
abstract = {Microorganisms, including bacteria, archaea, fungi, and viruses, are the most taxonomically diverse and ecologically dominant life forms on Earth, playing critical roles in ecosystems, human health, and industrial applications. While existing microbial databases such as BV-BRC and IMG archive both monoisolate and metagenome-assembled genomes (MAGs) across domains, challenges remain in standardized, multi-level annotations and interactive tools for all microbial groups. Here, we present MicrobialScope (https://microbial.deepomics.org/), a comprehensive microbial genomic platform that integrates large-scale genome collections, multilevel annotations, and interactive visualizations. MicrobialScope harbors 2 411 503 bacterial, 24 472 archaeal, 20 203 fungal, and 188 267 viral genomes derived from both monoisolate assemblies and MAGs. Integrating 15 state-of-the-art bioinformatics tools and 10 specialized databases, MicrobialScope provides extensive annotations encompassing basic genomic features, genomic element prediction (e.g., genes, tRNAs, tmRNAs, CRISPR-Cas and anti-CRISPR elements, secondary metabolite biosynthetic clusters, signal peptides, and transmembrane proteins), and functional and structural annotations. This includes 1 072 114 935 proteins with diverse annotations, 24 640 186 tRNAs and tmRNAs, 140 888 CRISPR-Cas systems, 173 256 anti-CRISPR elements, 105 121 secondary metabolite biosynthetic clusters, 13 235 096 signal peptides, and 50 811 729 transmembrane proteins. In addition, MicrobialScope offers unrestricted access to all data resources, interactive visualization tools, and built-in online analytical modules for intuitive exploration and comparative analysis. With its extensive genome collection, comprehensive annotations, and user-friendly interface, MicrobialScope serves as a scalable platform to advance genome research across diverse microbial domains.},
}

*Molecular Sequence Annotation
Archaea/genetics
*Databases, Genetic
Fungi/genetics
Genome, Viral
Genome, Archaeal
Bacteria/genetics
Viruses/genetics
*Genomics/methods
*Software
Genome, Fungal
Genome, Bacterial
Computational Biology/methods
Metagenome

@article {pmid41261732,
year = {2026},
author = {Fullam, A and Letunic, I and Maistrenko, OM and Castro, AA and Coelho, LP and Grekova, A and Schudoma, C and Khedkar, S and Robbani, M and Kuhn, M and Schmidt, TSB and Bork, P and Mende, DR},
title = {proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D852-D857},
pmid = {41261732},
issn = {1362-4962},
support = {FT230100724//Australian Research Council/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; LIBIS/de.NBI//Ministry of Science, Research and Art Baden-Württemberg/ ; //MEXT/ ; //Keio University/ ; },
mesh = {*Molecular Sequence Annotation/methods ; *Genome, Bacterial ; *Software ; *Databases, Genetic ; *Genomics/methods ; *Genome, Archaeal ; *Genome, Microbial ; Multigene Family ; },
abstract = {The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands robust quality control and consistent annotation pipelines to ensure meaningful biological insights. proGenomes4 (prokaryotic Genomes v4) addresses this challenge by providing a resource of nearly 2 million high-quality microbial genomes, a doubling in scale from previous versions, encompassing over 7 billion genes. Each genome underwent rigorous quality assessment and comprehensive functional annotation by applying multiple standardized annotation workflows, including the systematic identification of mobile genetic elements and biosynthetic gene clusters. proGenomes4 contains 32 887 species with ecological habitat metadata as well as precomputed pan-genomes. This substantially expanded resource provides the microbiology community with a foundation for large-scale comparative studies and is freely accessible via a newly developed command line interface and at https://progenomes.embl.de/.},
}

*Molecular Sequence Annotation/methods
*Genome, Bacterial
*Software
*Databases, Genetic
*Genomics/methods
*Genome, Archaeal
*Genome, Microbial
Multigene Family

@article {pmid41207298,
year = {2026},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D763-D775},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Metagenome
*Databases, Genetic
Molecular Sequence Annotation
Bacteria/genetics/classification
Software
Internet

@article {pmid41171142,
year = {2026},
author = {Lyu, B and Wu, K and Huang, Y and Anton, M and Li, X and Viknander, S and Anwer, D and Yang, Y and Lu, D and Kerkhoven, E and Zelezniak, A and Gao, D and Chen, Y and Li, F},
title = {GotEnzymes2: expanding coverage of enzyme kinetics and thermal properties.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D583-D592},
pmid = {41171142},
issn = {1362-4962},
support = {2024YFA0920300//National Key R&D Program of China/ ; 22478223//National Natural Science Foundation of China General Project/ ; A2403013//National Natural Science Foundation of China General Project/ ; JC2024004//Tsinghua Shenzhen International Graduate School/ ; DCE-iBHE-2023-1//Tsinghua Shenzhen International Graduate School/ ; 2023-04254//Swedish Research Council/ ; 2019-05356//Swedish Research Council/ ; 2019-01403//Formas grant/ ; BB/Y000730/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Kinetics ; *Enzymes/chemistry/metabolism ; *Databases, Protein ; Temperature ; Enzyme Stability ; Humans ; },
abstract = {Enzyme kinetics are fundamental for understanding metabolism, yet experimentally measured parameters remain scarce. To address this gap, we introduce GotEnzymes2, a substantially expanded resource covering 10 765 species, 7.3 million enzymes, and 59.6 million unique entries. Compared with the first version, GotEnzymes2 now integrates both catalytic and thermal parameters, enabling unified predictions of kcat, Km,kcat/Km, optimal temperature, and melting temperature. This expansion markedly broadens species and enzyme coverage, creating the most comprehensive database of enzyme kinetic and stability parameters to date. To construct the resource, we systematically benchmarked state-of-the-art models for catalytic and thermal parameter prediction, and incorporated the best-performing strategies to ensure accuracy and generalizability. Altogether, GotEnzymes2 provides the community with a powerful resource for data-driven enzyme discovery, design, and engineering, with broad applications in systems biology, metabolic engineering, and synthetic biology. GotEnzymes2 is publicly accessible at https://metabolicatlas.org/gotenzymes.},
}

Kinetics
*Enzymes/chemistry/metabolism
*Databases, Protein
Temperature
Enzyme Stability
Humans

@article {pmid41171134,
year = {2026},
author = {Sun, Y and Chen, Q and Fan, G and Sun, Q and Zhou, Q and Zhang, J and Nie, J and Ma, J and Wu, L},
title = {gcMeta 2025: a global repository of metagenome-assembled genomes enabling cross-ecosystem microbial discovery and function research.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D724-D733},
pmid = {41171134},
issn = {1362-4962},
support = {2021YFA0717001//National Key R&D Program of China/ ; XDB0830000//Chinese Academy of Sciences/ ; 153211KYSB201900211//Chinese Academy of Science/ ; //Chinese Academy of Sciences/ ; },
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Databases, Genetic ; Humans ; *Ecosystem ; Animals ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; },
abstract = {The rapid growth of metagenomic sequencing has generated an unprecedented wealth of metagenome-assembled genomes (MAGs), transforming opportunities for microbial discovery and functional characterization. Yet, full utilization of these resources has been constrained by heterogeneous data generation practices and inconsistent analytical pipelines. The gcMeta database addresses this gap by compiling MAGs through both public acquisition and de novo assembly. This release integrates over 2.7 million MAGs from 104 266 samples spanning various biomes, covering human, animal, plant, marine, freshwater, and extreme environments. It establishes 50 biome-specific MAG catalogues comprising 109 586 species-level clusters, of which 63% (69 248) represents previously uncharacterized taxa, and annotates >74.9 million novel genes. By linking functional traits with microbial co-occurrence networks, gcMeta identifies keystone taxa central to biogeochemical cycling and environmental adaptation. The platform further supports cross-ecosystem functional comparisons, revealing niche-specific metabolic pathways and stress-response genes. Moreover, gcMeta provides standardized, AI-ready datasets encompassing microbial enzymes, anti-phage defense systems, and other functional modules, enabling advanced machine learning applications. By bridging microbial "sequence discovery" with "functional utilization," gcMeta establishes a foundation for ecological research, industrial biotechnology, and novel gene mining. The platform is freely accessible at https://gcmeta.wdcm.org/.},
}

*Metagenome/genetics
*Metagenomics/methods
*Databases, Genetic
Humans
*Ecosystem
Animals
Molecular Sequence Annotation
Bacteria/genetics/classification

@article {pmid41171124,
year = {2026},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D813-D825},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Metagenome ; *Databases, Genetic ; *Microbiota/genetics ; Metagenomics/methods ; *Aquatic Organisms/genetics/classification ; Oceans and Seas ; *Seawater/microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics/classification ; Molecular Sequence Annotation ; Software ; Multiomics ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}

Metagenome
*Databases, Genetic
*Microbiota/genetics
Metagenomics/methods
*Aquatic Organisms/genetics/classification
Oceans and Seas
*Seawater/microbiology
Biodiversity
Ecosystem
Bacteria/genetics/classification
Molecular Sequence Annotation
Software
Multiomics

@article {pmid41160887,
year = {2026},
author = {Guo, S and Jiang, Y and Zou, J and Lu, M and Li, D and Zhang, Q and Li, W and Mao, L and Xu, Z and Liu, S},
title = {GPSAdb 2.0: an expanded atlas of gene-perturbation transcriptomes with enhanced tools for regulatory gene discovery.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1082-D1086},
pmid = {41160887},
issn = {1362-4962},
support = {82403086//National Natural Science Foundation of China/ ; CSTB2022NSCQ-BHX0698//Natural Science Foundation of Chongqing/ ; //Chongqing Medical Scientific Research Project/ ; 2025DBXM005//Chongqing Health Commission and Science and Technology Bureau/ ; CYYY-DSTDXM202502//Chongqing Medical University/ ; },
mesh = {Humans ; *Transcriptome ; *Software ; *Gene Expression Profiling/methods ; Gene Knockdown Techniques ; *Gene Expression Regulation ; Cell Line ; *Databases, Genetic ; },
abstract = {Gene perturbation is essential for uncovering gene function and its involvement in various biological processes and diseases. GPSAdb 2.0 (https://www.gpsadb.com/) presents a significantly expanded and improved platform for exploring gene expression changes following gene knockdown across diverse cell lines. Compared to GPSAdb 1.0, this new version offers several key upgrades: (i) a substantial increase in data coverage, now featuring 7665 gene knockdown groups, 42 235 samples, and 2810 perturbation genes across a broader array of cell lines and biological conditions; (ii) the introduction of new tools, including "BioTrigger" for flexible gene set enrichment analysis and "fastGPSA" for rapid, advanced differential expression analysis. With these enhancements, GPSAdb 2.0 provides researchers with a powerful resource for investigating gene perturbation effects and gaining deeper insights into transcriptional regulation, making it an invaluable resource for studies on gene regulation, disease mechanisms, and potential therapeutic targets.},
}

Humans
*Transcriptome
*Software
*Gene Expression Profiling/methods
Gene Knockdown Techniques
*Gene Expression Regulation
Cell Line
*Databases, Genetic

@article {pmid40874445,
year = {2026},
author = {Liang, M and Pan, W and Feng, Z and Cui, Y and Su, H and Guo, C and He, J},
title = {IVCDB: a comprehensive database of iridoviruses for epidemiology, genetic evolution, and disease management.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D790-D800},
pmid = {40874445},
issn = {1362-4962},
support = {2022YFE0203900//National Key Research and Development Program of China/ ; CARS-46//Earmarked Fund for China Agriculture Research System/ ; 32473201//National Natural Science Foundation of China/ ; 2022B1111030001//Special Project for Research and Development in Key areas of Guangdong Province/ ; 2024B1212040007//Science and Technology Planning Project of Guangdong Province/ ; 2023A1515110395//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Animals ; *Iridovirus/genetics/classification/pathogenicity ; Phylogeny ; Genome, Viral ; *Databases, Genetic ; *Evolution, Molecular ; *DNA Virus Infections/epidemiology/virology/veterinary ; Viral Proteins/genetics ; },
abstract = {Iridoviruses, a globally distributed group of double-stranded DNA viruses, exhibit remarkable environmental adaptability and host-switching capabilities, infecting over 200 species of ectothermic vertebrates and invertebrates, including reptiles, amphibians, fish, crustaceans, and insects. These characteristics have led to substantial economic losses in global aquaculture and population declines in amphibian and invertebrate species. Despite accumulating genomic data, research progress remains constrained by three critical limitations: fragmented multidimensional data resources, ambiguous taxonomic levels, and insufficient spatiotemporal visualization tools. To address these challenges, we present the Iridovirus Comprehensive Database (IVCDB; https://www.iridovirus.com/), a comprehensive database consolidating multidimensional iridovirus-related data. IVCDB provides curated comprehensive information on 310 geographically distinct virus isolates complemented by an interactive geospatial visualization system and a nonredundant protein database containing 4378 viral proteins, including 162 core genes/proteins, derived from a standardized genome annotation pipeline. This database also contains phylogenetic relationships across various viral taxonomic levels within the family Iridoviridaeanda viral genome collinearity analysis tool, facilitating taxonomic analysis and supporting novel species identification. Furthermore, IVCDB integrates an application-oriented knowledge base including host range data, experimentally validated vaccines, and field-deployable visual detection methods. IVCDB offers substantial support for disease control and host conservation while addressing systemic bottlenecks in viral cross-species transmission research.},
}

Animals
*Iridovirus/genetics/classification/pathogenicity
Phylogeny
Genome, Viral
*Databases, Genetic
*Evolution, Molecular
*DNA Virus Infections/epidemiology/virology/veterinary
Viral Proteins/genetics

@article {pmid41538792,
year = {2026},
author = {Kurilla, A and Čavojská, N and Ikegwuonu, T and Nemčíková, M and Schulte-Strathaus, JC and Uyttebroek, L and Beames, JR and Breznoščáková, D and Dančík, D and Hajdúk, M and Heretik, A and Izáková, Ľ and Katreniaková, Z and Myin-Germeys, I and Pečeňák, J and Reininghaus, U and Schick, A and Wolters, M},
title = {Preferences for an Experience Sampling Method-Based Tool as an Adjunct to Usual Treatment in Patients With Problem Substance Use: Qualitative Study.},
journal = {JMIR formative research},
volume = {10},
number = {},
pages = {e79510},
doi = {10.2196/79510},
pmid = {41538792},
issn = {2561-326X},
mesh = {Humans ; Male ; Female ; Adult ; Qualitative Research ; *Substance-Related Disorders/therapy/psychology ; *Patient Preference/psychology ; Middle Aged ; Adolescent ; Young Adult ; Europe ; Telemedicine ; Mental Health Services ; },
abstract = {BACKGROUND: Mobile health tools that use the Experience Sampling Method (ESM) appear to be a promising tool to streamline and improve the treatment of substance use disorders. However, patient involvement in the development of these tools is uncommon, and research on the preferences of people being treated for substance use disorders has been scarce. In the scope of the European Union IMMERSE (Implementing Mobile Mental health Recording Strategy for Europe) consortium, an ESM-based tool for Digital Mobile Mental Health (DMMH) was first codeveloped and later tested in 4 European countries.

OBJECTIVE: This study aimed to achieve an understanding of preferences for features of DMMH among mental health service users with problem substance use.

METHODS: In 4 European countries, service users were recruited for a semistructured qualitative interview, which started with the presentation of a prototype of the DMMH. Data analysis was performed through directed qualitative content analysis.

RESULTS: The analytical sample consisted of 12 (5 female, 6 male, and 1 nonbinary person) participants with problem substance use aged 18-50 years. There were 4 participants from Slovakia, 3 from Belgium, 4 from Germany, and 1 from Scotland. Patient preferences were classified into 7 categories: notifications, questions, user interface, functionality changes, visualizations, sharing data with clinicians, and sharing data with others. The proposed intensive notification schedule was deemed acceptable by service users as long as the questionnaire is short. Participants expressed a preference for open-text response options, Ecological Momentary Interventions, and options for individual customization of several elements of the tool. Data visualization was considered an important aid for communication with clinicians, with whom all participants wanted to share data obtained with DMMH. The possibility of sharing data with other people depended on the quality of the relationship with them.

CONCLUSIONS: In the development of ESM-based mobile health tools for people with problem substance use, their preferences for content, functionality, and appearance of the tools should be considered so they match patients' treatment needs.},
}

Humans
Male
Female
Adult
Qualitative Research
*Substance-Related Disorders/therapy/psychology
*Patient Preference/psychology
Middle Aged
Adolescent
Young Adult
Europe
Telemedicine
Mental Health Services

@article {pmid41538474,
year = {2026},
author = {Chami, AM and Zózimo, TRS and Matosinho, CGR and Silva-Filho, ALD and Carvalho, MRS and Braga, LDC},
title = {Characterization of a novel MSH2 variant in Lynch syndrome: clinical data and complementary bioinformatics assessment.},
journal = {Einstein (Sao Paulo, Brazil)},
volume = {24},
number = {},
pages = {eAO0757},
pmid = {41538474},
issn = {2317-6385},
mesh = {Humans ; *MutS Homolog 2 Protein/genetics ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology ; Female ; Computational Biology ; Middle Aged ; Pedigree ; Germ-Line Mutation/genetics ; Immunohistochemistry ; Phenotype ; Male ; },
abstract = {OBJECTIVE: To describe the clinical characteristics and perform a multi-step bioinformatics evaluation of the pathogenicity of NM_000251.3(MSH2):c.1894_1898del (p.Ile633Lysfs*9), an MSH2 germline variant detected in a family with Lynch syndrome.

METHODS: Clinical evaluation included description of phenotype, family history, and immunohistochemical characterization of the proband's tumors. For pathogenicity classification according to the American College of Genetics and Genomics/Association for Molecular Pathology (ACMG/APA) criteria, bioinformatics analyses included: (i) literature and database screening, searching for the variant allele frequency, case reports, or functional studies, including ClinVar, VarSome, Ensembl, PubMed, EVA, and ABraOM; (ii) prediction of variant impacts using ExPASy Translate, Pfam, and Modeller 9.24; and, (iii) mechanisms that could mitigate the effects of the variant included alternative splicing and exon skipping (UniProt and GTex) and nonsense-mediated decay (NMD; MutationTaster2021).

RESULTS: The proband, a 55-year-old female, was diagnosed with two metachronous colorectal cancers. Immunohistochemical analysis showed loss of expression (MSH2 in one tumor, and MSH2 and MSH6 in the other). Seven deceased family members were diagnosed with cancer (four colorectal, one uterine, and two unspecified). This variant caused a stop codon in MSH2 exon 12 of 16. When translated, the protein loses 294 C-terminal residues, which may prompt protein degradation. If the mutated protein escapes degradation, dimerization and DNA-binding domains will be present. Therefore, negative dominance effects were possible. No isoforms ending in exon 12 have been identified in the literature or in RNA splicing databases. A stop codon before the last exon-exon boundary indicated the occurrence of NMD.

CONCLUSION: No evidence of protein-rescuing mechanisms was found, supporting the classification of this variant as likely pathogenic/pathogenic.},
}

Humans
*MutS Homolog 2 Protein/genetics
*Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/pathology
Female
Computational Biology
Middle Aged
Pedigree
Germ-Line Mutation/genetics
Immunohistochemistry
Phenotype
Male

@article {pmid41525703,
year = {2026},
author = {Astill Wright, L and Roe, J and Guo, B and Morriss, R},
title = {Dropout, Attrition, Adherence, and Compliance in Mood Monitoring and Ambulatory Assessment Studies for Depression and Bipolar Disorder: Systematic Review and Meta-Analysis.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e83765},
pmid = {41525703},
issn = {2368-7959},
mesh = {Humans ; Affect ; *Bipolar Disorder/diagnosis ; *Depressive Disorder/diagnosis ; *Monitoring, Ambulatory/statistics & numerical data ; *Patient Compliance/statistics & numerical data ; *Patient Dropouts/statistics & numerical data ; },
abstract = {BACKGROUND: Ambulatory assessment and mood monitoring are different methods that can use novel technology to deliver a more efficient, flexible, and usable method of clinical outcome assessment compared with established measures of behavior and mood. Concerns have been raised around attrition in and adherence to these new protocols, particularly over the medium to long term by people with mood disorders.

OBJECTIVE: This systematic review and meta-analysis assessed attrition from and adherence to active and passive ambulatory assessment and mood monitoring protocols by people with bipolar disorder and depression over the medium and long term.

METHODS: Randomized controlled trials and nonrandomized studies were identified and rated for risk of bias. Adherence and attrition data were pooled to calculate effect sizes. We analyzed specific factors that we hypothesized a priori could affect the prevalences of attrition and adherence by means of subgroup meta-analysis or metaregression modeling.

RESULTS: We evaluated 77 mood tracking or ambulatory assessment studies including 17,123 participants. Pooled adherence was 0.64% (95% CI 0.59%-0.70%; P<.001), and pooled attrition was 0.28% (95% CI 0.22%-0.34%; P<.001). Three factors had a statistically significant subgroup difference for adherence: The presence of financial incentives increased adherence, and the presence of mood monitoring reminders and a higher study risk of bias decreased adherence. Four factors had a statistically significant subgroup difference for attrition: Digital mood monitoring decreased attrition versus analogue studies, but mood monitoring reminders, mood monitoring versus other protocols, and a high risk of study bias increased attrition. These analyses, however, were vulnerable to confounding by study design and protocol design. Attrition rates were not reported by 17 studies (17/77, 22%), and 20 studies (20/77, 26%) did not report adherence rates. Most studies had a low-to-moderate risk of bias, but heterogeneity was very high. Only 16 studies reported adherence systematically.

CONCLUSIONS: Reporting of attrition and adherence to ambulatory assessments was not systematic nor universal, and until it is, analyses are unlikely to demonstrate clear conclusions. We found very high heterogeneity and evidence of publication bias, and this limited the certainty of our conclusions. Financial incentives may increase adherence, and attrition may be lower in digital than analogue studies of mood monitoring. There was no statistically significant difference in adherence and attrition between studies of passive and active ambulatory assessments. Reminders of mood monitoring increased attrition and decreased adherence, but the results may be confounded by longer length of follow-up versus other studies.},
}

Humans
Affect
*Bipolar Disorder/diagnosis
*Depressive Disorder/diagnosis
*Monitoring, Ambulatory/statistics & numerical data
*Patient Compliance/statistics & numerical data
*Patient Dropouts/statistics & numerical data

@article {pmid41397974,
year = {2025},
author = {Zheng, F and Yao, W and He, W and Zhang, W and Chen, Y and Chen, H and Zeng, Z and Liu, XL and Ding, S and Zheng, Y and Huang, L and Zhu, Y and Zhang, C},
title = {A comprehensive database for high-throughput identification of archaeal lipids using high-resolution mass spectrometry.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {588},
pmid = {41397974},
issn = {2041-1723},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42372354//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Archaea/chemistry/metabolism ; *Lipids/chemistry/analysis ; *Mass Spectrometry/methods ; *Lipidomics/methods ; Tandem Mass Spectrometry/methods ; *Databases, Factual ; *Membrane Lipids/chemistry ; },
abstract = {Archaeal membrane lipids are markedly distinct from those in bacteria and eukaryotes, serving as biomarkers for unraveling their ecological and biogeochemical roles. Recent advancements in high-resolution mass spectrometry-based lipidomic research facilitate detailed cellular-level characterizations of lipid compounds. However, the lack of a comprehensive and dedicated database severely limits large-scale, high-throughput investigations of archaeal lipids. We present ArchLips, a comprehensive database containing 219,348 in silico molecular structures and tandem mass spectra of 199,248 corresponding archaeal lipid compounds. ArchLips enables the automatic and accurate annotation of archaeal lipid compounds characterized by high-resolution mass spectrometry from both pure cultures and environmental samples, serving as a transformative tool for enhancing our understanding of archaeal diversity and its ecological and evolutionary significance within global ecosystems.},
}

*Archaea/chemistry/metabolism
*Lipids/chemistry/analysis
*Mass Spectrometry/methods
*Lipidomics/methods
Tandem Mass Spectrometry/methods
*Databases, Factual
*Membrane Lipids/chemistry

@article {pmid41391105,
year = {2026},
author = {Edwards, CJ and Smith, R and Lafit, G and Ward, T and Emsley, R and Rus-Calafell, M and Myin-Germeys, I and Peters, E and Bucci, S and Craig, TK and Haddock, G and Ball, H and Fornells-Ambrojo, M and Hardy, A and McLeod, H and Gumley, AI and McDonnell, J and Montague, A and Clancy, M and Huckvale, M and Garety, PA},
title = {The Impact of AVATAR Therapy on Voice Hearing in Everyday Life: ESM Outcomes of the AVATAR2 Trial.},
journal = {Schizophrenia bulletin},
volume = {52},
number = {1},
pages = {},
doi = {10.1093/schbul/sbaf100},
pmid = {41391105},
issn = {1745-1701},
support = {215471/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Female ; Male ; Single-Blind Method ; Adult ; Middle Aged ; *Hallucinations/therapy ; *Ecological Momentary Assessment ; *Outcome Assessment, Health Care ; Follow-Up Studies ; Young Adult ; *Psychotherapy/methods ; Avatar ; },
abstract = {AVATAR therapy involves facilitated dialogs between a voice hearer and a digital embodiment of their distressing voice ("the avatar"). We conducted a multi-site single-blind randomized controlled trial to evaluate the efficacy of brief (AV-BRF) and extended (AV-EXT) forms of AVATAR therapy, compared with treatment as usual (TAU) alone (AVATAR2). This study reports the data from experience sampling method (ESM) assessments conducted at baseline, end of therapy (16 weeks), and follow-up (28 weeks). The research questions focused on whether those in the AV-BRF or AV-EXT arms experienced less voice-related distress, anxiety, and beliefs as measured by ESM, compared to TAU. Separate mixed-effects models were fitted for each research question. The final sample (n = 200) completed approximately 40% of questionnaires across all timepoints. Participants who received AV-EXT therapy, but not AV-BRF, reported reduced momentary voice-related distress at 16 (P = .022) and 28 weeks (p = .029). Appraisals of voice control were also reduced in the AV-EXT arm at 16 weeks when the voice was present (P = .002) or not (P = .008). Voice power appraisals were reduced (P < .035) in both arms when the voice was "not present but on my mind" at all timepoints. There were no changes in the frequency of voice hearing, appraisals of voice intent, or assertive responding. These findings from everyday life, reported for the first time, provide evidence of the impact on the primary AVATAR therapy treatment targets, including appraisals of voice power and control. The weight of evidence favors the AV-EXT protocol in the further development and implementation of AVATAR therapy.},
}

Humans
Female
Male
Single-Blind Method
Adult
Middle Aged
*Hallucinations/therapy
*Ecological Momentary Assessment
*Outcome Assessment, Health Care
Follow-Up Studies
Young Adult
*Psychotherapy/methods
Avatar

@article {pmid41532084,
year = {2026},
author = {Carvalho, PC and Voltolini, GB and Goedert, A and Chiaratti, VKC and Cantarelli, EH and Francisco, JC and Almeida, TB and Burigo, IP},
title = {Hospitalizations due to Alzheimer's disease in Brazil during the COVID-19 pandemic: an update on frequency, mortality, and costs.},
journal = {Dementia & neuropsychologia},
volume = {20},
number = {},
pages = {e20250322},
doi = {10.1590/1980-5764-DN-2025-0322},
pmid = {41532084},
issn = {1980-5764},
abstract = {UNLABELLED: Hospitalizations related to Alzheimer's disease (AD) impose a growing burden on health systems, but recent, nationally representative estimates for Brazil are limited.

OBJECTIVE: To describe the epidemiological profile of hospital admissions due to AD in Brazil from 2018 to 2024.

METHODS: Ecological time-series study using the Hospital Information System of the Brazilian Unified Health System (SIH/SUS), accessed via the Department of Informatics of the SUS (DATASUS). We included all regions and states from January 2018 to December 2024. Admissions were identified by the International Classification of Diseases, 10[th] Revision (ICD-10) codes G30.0-G30.9 and F00.0-F00.9. Variables comprised sex, age group, race/color, admission type (urgent/elective), in-hospital mortality, length of stay, and hospital costs. Temporal trends were evaluated with linear regression.

RESULTS: From 2018 to 2024, 11,212 AD-related hospitalizations were recorded; 79.4% were urgent. The Southeast had the highest absolute number (47.8%), followed by the South (25.1%), Northeast (17.2%), Midwest (6.5%), and North (3.4%). Females accounted for 65% of admissions and 64.7% of in-hospital deaths. Older adults, especially those ≥80 years, represented most hospitalizations (59.3%) and deaths (69.7%). Total hospital expenditures exceeded R$ 14 million, with the Southeast concentrating >60% of national costs. No significant linear trend was detected in annual rates.

CONCLUSION: Urgent admissions comprised the majority of AD hospitalizations nationwide, with the Southeast presenting the highest numbers. The predominance of older female patients and high in-hospital mortality underscore the need for targeted clinical and public health strategies. Rising expenditures reinforce investment in health infrastructure and long-term dementia-care policies in Brazil.},
}

@article {pmid41531076,
year = {2026},
author = {Liu, PD and Huang, L and Meng, F and Zhao, HH and Liu, JT},
title = {[Multi-scenario Prediction and Ecological Security Pattern Construction Based on InVEST-PLUS Model: A Case Study of Liaoning Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {467-480},
doi = {10.13227/j.hjkx.202412160},
pmid = {41531076},
issn = {0250-3301},
abstract = {Taking policy factors into account in constructing an ecological security pattern is of great significance in helping to realize the ecological civilization strategy. Taking Liaoning Province as an example， the study adopts a research framework of "core-regional-strip-multi-point" based on five land use data sets from 2000 to 2020 and couples the InVEST-PLUS model to predict the land use and carbon storage in the SN， SW， CLD， and SE scenarios for the year 2030. The study then combines the MSPA and MCR models to construct an ecological security pattern and proposes new ideas for ecological construction. The results showed that： ① The land use prediction results indicated that land use was mainly composed of farmland and forests. The farmland area decreased slowly， and the forest area increased continuously from 2000 to 2030. ② The spatial distribution of carbon storage was mainly in the east， and the eastern region was a key protected forest area. The trend of carbon storage in the eastern region was relatively stable， while the carbon storage in the western region continued to increase. ③ The ecological security network structure in the SE scenario was complex and highly connected， identifying 30 ecological source areas， 97 discontinuities， 56 ecological corridors with a total length of 211 km， and a northeastern-southeastern strip-shaped extension pattern with dense networks in the middle and western regions and sparse networks in the eastern coastal areas. ④ Comparing the structure and connectivity of the ecological security network in different scenarios， the study selected the SE scenario and proposed the "one core， three regions， three belts， and multiple points" ecological security pattern construction strategy. It also proposed ecological management policy recommendations to promote sustainable development in Liaoning Province.},
}

@article {pmid41480951,
year = {2026},
author = {Zhang, S and Jiao, Z and Liu, Z and Peng, Z and Cui, L and Hu, Z and Jiao, Z and Yuan, Q and Qiu, Z and Yan, C},
title = {Multiomics Analysis Revealed the Role of LsBBX22-LsHY5a/b Module in Promoting UV-B-Mediated Anthocyanin Accumulation in Lettuce.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {1},
pages = {1788-1803},
doi = {10.1021/acs.jafc.5c08530},
pmid = {41480951},
issn = {1520-5118},
mesh = {*Anthocyanins/biosynthesis/metabolism ; *Lactuca/metabolism/genetics/radiation effects ; Ultraviolet Rays ; *Plant Proteins/genetics/metabolism ; Gene Expression Regulation, Plant/radiation effects ; *Transcription Factors/metabolism/genetics ; Multiomics ; },
abstract = {Ultraviolet-B (UV-B) radiation profoundly affects plant photomorphogenesis and secondary metabolism, yet its regulatory role in lettuce (Lactuca sativa) remains poorly understood. We conducted metabolome and transcriptome analyses to reveal the molecular basis of UV-B adaptation in highland-grown lettuce. Flavonoid accumulation was enhanced as a key adaptive strategy for UV-B acclimation. The key UV-B signaling components LsHY5a/b showed positive correlations with ten LsBBXs and flavonoid/anthocyanin-related genes. UV-B treatment rapidly induced the transcription of LsHY5a/b and LsBBX22-1. LsBBX22-1 physically interacted with LsHY5a/b. While LsBBX22-1 activated the expression of anthocyanin-related genes, it could not bind directly to their promoters. By contrast, LsHY5a/b directly bound to the promoters of LsCHS1, LsCHI3, and LsF3H. Thus, LsBBX22 and LsHY5a/b acted synergistically to regulate UV-B-induced anthocyanin biosynthesis. This study clarified the molecular mechanism of the LsBBX22-1-LsHY5a/b module in promoting UV-B-induced anthocyanin accumulation in lettuce, providing a theoretical basis for cultivating high-quality vegetables in highland regions.},
}

*Anthocyanins/biosynthesis/metabolism
*Lactuca/metabolism/genetics/radiation effects
Ultraviolet Rays
*Plant Proteins/genetics/metabolism
Gene Expression Regulation, Plant/radiation effects
*Transcription Factors/metabolism/genetics
Multiomics

@article {pmid41529120,
year = {2026},
author = {Li, J and Chen, S and Wu, Z and Wang, H and Xia, R and Meng, J and Zhang, Y},
title = {CircRM: profiling circular RNA modifications from nanopore direct RNA sequencing.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf726},
pmid = {41529120},
issn = {1477-4054},
mesh = {*RNA, Circular/genetics/metabolism ; Humans ; *Sequence Analysis, RNA/methods ; *Nanopore Sequencing ; *RNA Processing, Post-Transcriptional ; Computational Biology/methods ; },
abstract = {Circular RNA (circRNA) represents a critical class of regulatory RNAs with distinctive structural and functional features. The functions of circRNAs are modulated by various RNA modifications. Here, we present CircRM, a nanopore direct RNA sequencing-based computational method for profiling RNA modifications in circRNAs at single-base and single-molecule resolution. By integrating circRNA detection, read-level modification detection, and quantitative assessment of methylation rates, CircRM identified 427 high-confidence circRNAs and enables systematic characterization of three major modifications, m5C (AUC = 0.855), m6A (AUC = 0.817) and m1A (AUC = 0.769). It revealed distinct modification patterns compared with linear RNAs, highlighting RNA-type-specific regulations. We also identified the key features of circRNA-specific modifications, such as the enrichment near the back-splice junctions. Cross-cell line analyses further demonstrated conserved and cell-type-specific modification patterns. Together, these findings reveal, at the computational level, a unique epitranscriptomic landscape associated with circRNAs and establish CircRM as a powerful tool for advancing the study of RNA modifications in circular RNA biology. CircRM is free accessible at: https://github.com/jiayiAnnie17/CircRM.},
}

*RNA, Circular/genetics/metabolism
Humans
*Sequence Analysis, RNA/methods
*Nanopore Sequencing
*RNA Processing, Post-Transcriptional
Computational Biology/methods

@article {pmid41276033,
year = {2026},
author = {Liu, XY and He, FX and Qu, TC and Weng, ZH and Li, PF and Ye, J and Fu, HY},
title = {Integrated physiological and multi-omics insights into Chlorella mutagenized by atmospheric and room temperature plasma for enhanced saline aquaculture wastewater treatment and bioresource production.},
journal = {Bioresource technology},
volume = {442},
number = {},
pages = {133694},
doi = {10.1016/j.biortech.2025.133694},
pmid = {41276033},
issn = {1873-2976},
mesh = {*Chlorella/genetics/physiology/metabolism/drug effects ; *Wastewater/chemistry ; *Aquaculture/methods ; *Water Purification/methods ; *Mutagenesis ; *Plasma Gases/pharmacology ; Nitrogen ; Salinity ; Photosynthesis ; Temperature ; Biological Oxygen Demand Analysis ; Phosphorus ; *Metabolomics/methods ; Chlorophyll/metabolism ; Multiomics ; },
abstract = {The salinity of aquaculture wastewater varies considerably across farming systems, limiting the applicability of conventional Chlorella strains. To enhance salt tolerance and application potential, atmospheric and room temperature plasma (ARTP) mutagenesis was employed for its high mutation efficiency and ability to generate genetically stable mutants via a non-thermal plasma process. Among five mutant strains evaluated, strain AMC-2 exhibited the best performance, with enhanced growth, photosynthesis, nutrient removal, and bioresource accumulation. Within 8 days, strain AMC-2 removed over 90 % of total nitrogen (TN) and total phosphorus (TP) and chemical oxygen demand (COD), with algal density and chlorophyll content increased by 110 % and 134 %, respectively. The maximum quantum yield of PSII photochemistry reached 0.78, and the maximum electron transport rate increased by 69 %. Protein, polysaccharide, and lipid contents were also elevated by 83 %, 32 %, and 12 %, respectively. Compared to the wild-type, transcriptomic and metabolomic analyses of AMC-2 revealed coordinated upregulation of key genes (e.g., LHCB1, rbcS, ALDO, GOT2, Nrt, and NR) and elevated levels of metabolites such as citric acid, isocitric acid, γ-aminobutyric acid, and glycerophospholipids. These changes indicate systemic reprogramming of photosynthesis, carbon and nitrogen metabolism, and membrane composition. Functional validation in saline aquaculture wastewater demonstrated that AMC-2 sustained stable growth, photosynthetic activity, and nutrient removal at salinities up to 15 ppt, confirming its enhanced environmental adaptability. Collectively, these results highlight AMC-2 as a promising microalgal candidate for integrated bioremediation and bioresource production in brackish aquaculture systems, and exemplify the effectiveness of ARTP mutagenesis for improving microalgal performance under challenging conditions.},
}

*Chlorella/genetics/physiology/metabolism/drug effects
*Wastewater/chemistry
*Aquaculture/methods
*Water Purification/methods
*Mutagenesis
*Plasma Gases/pharmacology
Nitrogen
Salinity
Photosynthesis
Temperature
Biological Oxygen Demand Analysis
Phosphorus
*Metabolomics/methods
Chlorophyll/metabolism
Multiomics

@article {pmid41525285,
year = {2026},
author = {Ramirez-Gil, JG and López-Hernández, F and Conejo-Rodriguez, DF and Henao-Rojas, JC and Quiroga-Benavides, KE and Cortés, AJ and Chacón-Sánchez, MI},
title = {GermVersity: A free and user-friendly interface to enhance the visualization and analysis of genebank data.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340826},
pmid = {41525285},
issn = {1932-6203},
mesh = {Genetic Variation ; Polymorphism, Single Nucleotide ; *User-Computer Interface ; *Databases, Genetic ; Phenotype ; *Seed Bank ; },
abstract = {Genebanks are crucial for food security and industrial applications. However, their heterogeneous nature hinders effective utilization. To address this, the GermVersity platform was developed to integrate conventional, artificial intelligence, and data science approaches to the transversal analysis of data associated with genebank accessions. GermVersity aids in the classification and prioritization of germplasm diversity, facilitating the conservation and utilization of valuable genetic resources in agriculture. The GermVersity proposal is focused on developing a user-friendly application to visualize, analyze and interpret analysis-ready data from genebanks. The application's case study uses data from the bean genebank at Bioversity International - CIAT but can be adapted for other genebanks and broader collections. GermVersity is divided into three modules. The first module analyzes genetic diversity using phenotypic and SNP data. In this module users can prioritize morphological descriptors for efficient classification of accessions, define genetic clusters or populations, calculate basic diversity statistics per locus and per population, and estimate genetic divergence among clusters or populations. The second module implements spatial distribution modeling, allowing users to understand ecological diversity across the geographical distribution range of a set of accessions. The third module characterizes the genomic architecture of phenotypic trait variation and adaptation to ecological niches using genome-wide association implemented in prediction integrated tools (GAPIT) and Latent Factor Mixed Model (LFMM) analysis. The GermVersity platform was built using Shiny-Golem and is hosted on GitHub for free use. To access it, users can install the library and run the application through specific commands in R. Responsible use of algorithms is recommended, along with the inspection of results for biological coherence. Ultimately, GermVersity offers an integrated analytical pipeline to leverage genebank diversity as part of pre-breeding efforts.},
}

Genetic Variation
Polymorphism, Single Nucleotide
*User-Computer Interface
*Databases, Genetic
Phenotype
*Seed Bank

@article {pmid41525251,
year = {2026},
author = {Palenova, E and Veraverbeke, S and Drobyshev, I and Kontos, T and Ebert, K},
title = {Prioritizing areas for post-fire restoration in Greece using mixed-methods spatial analysis.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339998},
pmid = {41525251},
issn = {1932-6203},
mesh = {Greece ; *Conservation of Natural Resources/methods ; *Spatial Analysis ; *Wildfires ; Geographic Information Systems ; Humans ; Climate Change ; *Fires ; },
abstract = {The Mediterranean region will likely face an increase in the frequency and intensity of wildfires due to climate change. Despite being fire-prone, Greece lacks a developed standardized system for identifying and prioritizing burned areas in relation to their restoration needs. Prioritization of areas for post-fire restoration efforts using Geographic Information System and Remote Sensing is a powerful decision-making tool, which, however, can be insufficient in effectively integrating socio-ecological criteria and perspectives from multiple stakeholders. Combining qualitative methods such as interviews with remotely sensed data can enhance the understanding of nuances in a local context. We designed an approach to identify high-priority areas for post-fire vegetation restoration. The identification was based on stakeholder interviews and the subsequent integration of their responses with subsequent multi-criteria overlay analysis. We selected criteria to rank the areas by interviewing 15 stakeholders working on post-fire issues. The expert interviews revealed the key characteristics respondents consider essential for prioritizing burned areas for restoration. Areas covering 77.25 km[2] were selected for restoration depending on the fire history, slope, and designation as part of the protected areas. Outcomes of the analysis helped to highlight three locations that potentially need special attention, with the total area of 31 km[2]. We propose a prioritization system that is flexible, scalable, and can help government agencies, local foresters, private consultancies, and NGOs plan restoration actions and optimize the effectiveness of restoration programs in various ecosystems.},
}

Greece
*Conservation of Natural Resources/methods
*Spatial Analysis
*Wildfires
Geographic Information Systems
Humans
Climate Change
*Fires

@article {pmid41523158,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Light Arches, Apamea lithoxylaea (Denis & Schiffermüller), 1775 (Lepidoptera: Noctuidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {508},
pmid = {41523158},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Apamea lithoxylaea (Light Arches; Arthropoda; Insecta; Lepidoptera; Noctuidae). The assembly contains two haplotypes with total lengths of 577.73 megabases and 521.26 megabases. Most of haplotype 1 (98.15%) is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 16.43 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41516498,
year = {2025},
author = {Výbošťok, J and Chudá, J and Tomčík, D and Gretsch, D and Tomaštík, J and Pełka, M and Bedkowski, J and Skladan, M and Mokroš, M},
title = {An Open and Novel Low-Cost Terrestrial Laser Scanner Prototype for Forest Monitoring.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {1},
pages = {},
pmid = {41516498},
issn = {1424-8220},
support = {09I03-03-V04-00341.//Recovery and Resilience Plan for Slovakia/ ; VEGA 1/0604/24//Ministry of Education of Slovak Republic/ ; VV-MVP-24-0412//Slovak Research and Development Agency/ ; },
abstract = {Accurate and efficient forest inventory methods are crucial for monitoring forest ecosystems, assessing carbon stocks, and supporting sustainable forest management. Traditional field-based techniques, which rely on manual measurements such as diameter at breast height (DBH) and tree height (TH), remain labour-intensive and time-consuming. In this study, we introduce and validate a fully open-source, low-cost terrestrial laser scanning system (LCA-TLS) built from commercially available components and based on the Livox Avia sensor. With a total cost of €2050, the system responds to recent technological developments that have significantly reduced hardware expenses while retaining high data quality. This trend has created new opportunities for broadening access to high-resolution 3D data in ecological research. The performance of the LCA-TLS was assessed under controlled and field conditions and benchmarked against three reference devices: the RIEGL VZ-1000 terrestrial laser scanner, the Stonex X120GO handheld mobile laser scanner, and the iPhone 15 Pro Max structured-light device. The LCA-TLS achieved high accuracy for estimating DBH (RMSE: 1.50 cm) and TH (RMSE: 0.99 m), outperforming the iPhone and yielding results statistically comparable to the Stonex X120GO (DBH RMSE: 1.32 cm; p > 0.05), despite the latter being roughly ten times more expensive. While the RIEGL system produced the most accurate measurements, its cost exceeded that of the LCA-TLS by a factor of about 30. The hardware design, control software, and processing workflow of the LCA-TLS are fully open-source, allowing users worldwide to build, modify, and apply the system with minimal resources. The proposed solution thus represents a practical, cost-effective, and accessible alternative for 3D forest inventory and LiDAR-based ecosystem monitoring.},
}

@article {pmid41515900,
year = {2025},
author = {Wu, J and Zhou, L and Qiu, D and Wei, T and Xie, C and Chen, E and Lin, M and Fan, Y},
title = {Integrating Bioinformatics and Experimental Validation Identifies SCD as a Ferroptosis-Related Immune Regulator and Therapeutic Target in Crohn's Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41515900},
issn = {1422-0067},
support = {2025J011410//the Natural Science Foundation of Fujian Province/ ; 2025J08298//the Natural Science Foundation of Fujian Province/ ; },
mesh = {*Ferroptosis/genetics/immunology ; *Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy ; *Computational Biology/methods ; Humans ; Animals ; Mice ; Disease Models, Animal ; Gene Expression Profiling ; Colitis/genetics/chemically induced/immunology ; },
abstract = {This study investigates the role of ferroptosis-related genes (FRGs) in the intestinal inflammation of Crohn's disease (CD). Through integrated bioinformatics and experimental validation, we identified differentially expressed genes from RNA-seq data and intersected them with known FRGs to obtain ferroptosis-related differentially expressed genes (FEDGs). Functional enrichment and immune infiltration analyses were performed, and seven hub FEDGs were selected using machine learning. A diagnostic model based on these genes showed strong predictive ability. Immune analysis revealed significant associations with macrophages, neutrophils, dendritic cells, and CD4+ T cells. Protein expression of key hub genes was validated in clinical CD samples and a DSS-induced colitis model. Importantly, localized inhibition of SCD alleviated disease severity in experimental colitis. These findings highlight the involvement of ferroptosis in CD immune dysregulation and propose SCD as a potential therapeutic target.},
}

*Ferroptosis/genetics/immunology
*Crohn Disease/genetics/immunology/metabolism/pathology/drug therapy
*Computational Biology/methods
Humans
Animals
Mice
Disease Models, Animal
Gene Expression Profiling
Colitis/genetics/chemically induced/immunology

@article {pmid41411345,
year = {2025},
author = {Fairbanks, EL and Baylis, M and Daly, JM and Tildesley, MJ},
title = {Quantifying vector diversion effects in zoonotic systems: A modelling framework for arbovirus transmission between reservoir and dead-end hosts.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013359},
doi = {10.1371/journal.pcbi.1013359},
pmid = {41411345},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Mosquito Vectors/virology ; Culex/virology ; *Disease Reservoirs/virology ; *Models, Biological ; West Nile Fever/transmission ; *Zoonoses/transmission/virology ; West Nile virus ; Computational Biology ; Vector Borne Diseases/transmission ; *Arbovirus Infections/transmission ; },
abstract = {Vector-borne disease transmission involves complex interactions between vectors, reservoir hosts and dead-end hosts. We present a mathematical model for the vectorial capacity that incorporates multiple host types and their interactions, focusing specifically on West Nile virus transmission by Culex pipiens mosquitoes. Our model integrates climate-dependent parameters affecting vector biology with vector control interventions to predict transmission potential under various scenarios. We demonstrate how vector control interventions targeting one host type can significantly impact transmission dynamics across all host populations. By examining the effects of different vector control tool modes of action (repellency, preprandial killing, disarming and postprandial killing), we develop target product profiles that minimise unintended consequences of vector control. Notably, we identify the optimal intervention characteristics needed to prevent repellency on dead-end hosts from inadvertently increasing transmission among reservoir hosts. This research provides valuable insights for public health officials designing targeted vector control strategies and offers a flexible modelling framework that can be adapted to other vector-borne diseases with complex host dynamics.},
}

Animals
Humans
*Mosquito Vectors/virology
Culex/virology
*Disease Reservoirs/virology
*Models, Biological
West Nile Fever/transmission
*Zoonoses/transmission/virology
West Nile virus
Computational Biology
Vector Borne Diseases/transmission
*Arbovirus Infections/transmission

@article {pmid41339657,
year = {2025},
author = {Yao, G and Cai, X and Liu, J and Ding, S and Chen, X and Lin, C and Li, X and Yang, D},
title = {Chromosome-level genome assembly of Anastoechus asiaticus (Diptera: Bombyliidae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {10},
pmid = {41339657},
issn = {2052-4463},
support = {31970435//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300372//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Chromosomes, Insect ; *Diptera/genetics ; *Genome, Insect ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {The genus Anastoechus plays a crucial role in ecosystems, functioning both as a pollinator and as a natural enemy, with its larvae parasitizing grasshopper egg masses and adults visiting flowers. Despite its ecological significance, research on Anastoechus remains limited. In this study, we present a chromosomal-level genome assembly of Anastoechus asiaticus, utilizing BGI sequencing, PacBio sequencing and High-throughput chromosome conformation capture (Hi-C) technology. This represents the first genomic data for the genus Anastoechus, with a final genome size of 512.14 Mb and a scaffold N50 of 82.71 Mb. Genome annotation identified 12,751 protein-coding genes, of which functional annotations are available for 11,305. Additionally, non-coding RNA annotation revealed 1,753 tRNAs, 56 miRNAs, 79 rRNAs, and 49 snRNAs. Repetitive elements account for 290.64 Mb, constituting 56.75% of the genome. This high-quality genome provides valuable data for future studies on population genetics, ecological adaptation, and the evolution of Bombyliidae and other related insect groups.},
}

Animals
*Chromosomes, Insect
*Diptera/genetics
*Genome, Insect
Molecular Sequence Annotation
Datasets as Topic

@article {pmid41495476,
year = {2026},
author = {Green, A and Ontiveros-Palacios, N and Jandalala, I and Panni, S and Wood, V and Antonazzo, G and Attrill, H and Bateman, A and Sweeney, B},
title = {GOFlowLLM-curating miRNA literature with large language models and flowcharts.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {1},
pages = {},
doi = {10.1093/bioinformatics/btaf683},
pmid = {41495476},
issn = {1367-4811},
support = {//European Union's Horizon 2020 Marie Skłodowska-Curie Actions/ ; UKRI746:24BBR//United Kingdom Research and Innovation (UKRI) Biotechnology and Biological Sciences Research Council/ ; MR/W024233/1/MRC_/Medical Research Council/United Kingdom ; 310300/Z/24/Z & 218236/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory/ ; },
mesh = {*MicroRNAs/genetics ; *Software ; Gene Ontology ; *Data Curation/methods ; Humans ; *Computational Biology/methods ; Molecular Sequence Annotation/methods ; Large Language Models ; },
abstract = {MOTIVATION: The exponential growth of non-coding RNA research-with over 230 000 papers published since 2000-has created an urgent knowledge management crisis in molecular biology. Despite their crucial regulatory roles, microRNAs (miRNAs) face a significant curation bottleneck, with only 1400 articles manually curated to the Gene Ontology (GO) knowledgebase over a decade. This highlights the critical need for automated systems that can accelerate biocuration while maintaining high-quality standards.

RESULTS: We present GOFlowLLM, an automated curation pipeline powered by reasoning-enabled Large Language Models (LLMs) that follows established GO curation flowcharts to extract and structure miRNA-mediated gene silencing data at scale. When evaluated on existing curation, GOFlowLLM selects the correct GO term in 90% of cases, with curators agreeing with 95% of the system's reasoning steps and 90% of the evidence selected. Applied to 6996 previously uncurated articles using the Qwen QwQ-32B model, our system identified 2538 new candidate GO annotations on 1785 articles in just 58 hours-potentially doubling the available miRNA GO curation. Manual review shows curators agreed with the selected term in 87% of cases, the model's reasoning in 92% of cases, and the extracted evidence in 93%. The integration of reasoning traces provides transparent justification for annotations that can be reviewed by human curators, addressing a key challenge in adopting AI for scientific curation.

GOFlowLLM is implemented as an automated pipeline that follows expert-designed reasoning frameworks to maintain curation quality. The system is available on GitHub: https://github.com/RNAcentral/GO_Flow_LLM.},
}

*MicroRNAs/genetics
*Software
Gene Ontology
*Data Curation/methods
Humans
*Computational Biology/methods
Molecular Sequence Annotation/methods
Large Language Models

@article {pmid41514910,
year = {2025},
author = {Abdullah, NI and Elias, N' and Ohte, N and Vincenot, CE},
title = {Bat Community Response to Insect Abundance in Relation to Rice Phenology in Peninsular Malaysia.},
journal = {Biology},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/biology15010069},
pmid = {41514910},
issn = {2079-7737},
support = {SS2011//Bat Conservation International/ ; ABDUMALA1220-00//Idea Wild/ ; RG-07012020/02//The Habitat Foundation/ ; },
abstract = {Bats provide essential ecosystem services, particularly in regulating insect populations within agricultural landscapes. However, research on bat-insect interactions in Malaysian rice fields remains limited. This study examined bat diversity and insect abundance in the rice field area of Gunung Keriang, Kedah, using two harp traps, two mist nets and a light trap at three selected sites. A total of 2499 bats representing 27 species were captured, alongside 161,539 insects from 11 orders. Rhinolophus pusillus was the dominant bat species across all seasons. During the dry season, Chilo polychrysus (stem borer) was the dominant insect pest, whereas Nilaparvata lugens (brown planthopper) prevailed during the wet season. Insects from the order Coleoptera, dominant in the dry season, are likely consumed by larger bat species with stronger bite forces. Bat foraging activity peaked concurrently with insect emergence, corresponding to periods of high food availability. Statistical analysis revealed significant associations between bat activity, temperature, and rainfall, but not insect abundance. These findings underscore the ecological importance of bats as natural pest regulators in rice field ecosystems and highlight their potential role in promoting sustainable, ecosystem-based agricultural management.},
}

@article {pmid41513569,
year = {2026},
author = {Narita, M and Matsugaki, R and Muramatsu, K and Fushimi, K and Matsuda, S},
title = {Corrigendum to "Obesity and risk of post-operative pneumonia among older adult patients with hip fracture: An obesity paradox" [Clin Nutr ESPEN 68 (2025) 342-347].},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102904},
doi = {10.1016/j.clnesp.2025.102904},
pmid = {41513569},
issn = {2405-4577},
}

@article {pmid41512284,
year = {2026},
author = {Nemoto, Y and Okawara, M and Nishizawa, N and Mori, M and Takenaka, M and Kuroda, K and Fujino, Y and Matsuda, S and Fushimi, K and Tanaka, F},
title = {Robotic versus video-assisted thoracoscopic lobectomy/segmentectomy: multilevel analysis in Japan.},
journal = {Interdisciplinary cardiovascular and thoracic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1093/icvts/ivag005},
pmid = {41512284},
issn = {2753-670X},
abstract = {OBJECTIVES: Large-scale comparative data on the perioperative safety of robotic-assisted thoracoscopic surgery and video-assisted thoracoscopic surgery in Asia are limited. We compared the perioperative outcomes of these two approaches for lung cancer.

METHODS: This retrospective study used data from the Diagnostic Procedure Combination database in Japan. We included 47,541 patients who underwent lobectomy or segmentectomy for lung cancer from 2018 to 2021 and performed multivariable analyses.

RESULTS: Among 47,541 patients, 2,835 underwent robotic-assisted thoracoscopic surgery. Perioperative mortality did not differ significantly between groups (incidence rate ratio, 1.71; 95% confidence interval, [0.88-3.33]). Robotic-assisted surgery was associated with longer anaesthesia time and a higher incidence of mechanical ventilation postoperatively (incidence rate ratio, 1.96; 95% confidence interval, [1.36-2.81]), although the absolute difference was small (Marginal risk difference, +0.52 percentage points; 95% confidence interval, +0.14 to + 0.91). No significant differences were observed in other major complications, reoperation, or hospital stay.

CONCLUSIONS: In this large, real-world Japanese cohort including the early experience with robotic surgery, overall perioperative safety was comparable between robotic-assisted and video-assisted thoracoscopic surgery, although a statistically significant but small absolute increase in postoperative ventilation was observed with the robotic approach. This association remained robust across a series of sensitivity analyses. However, it is likely influenced by unmeasured confounding. Future prospective studies should investigate specific procedural factors, including anaesthetic management, and patient selection to optimize outcomes.},
}

@article {pmid41419039,
year = {2026},
author = {Rozen-Rechels, D and Lemesle, P and Jouanneau, W and Sebastiano, M and Harris, SM and Blévin, P and Angelier, F and Gernigon, J and Lemesle, JC and Robin, F and Budzinski, H and Labadie, P and Bustamante, P and Chastel, O},
title = {How does habitat use influence PFAS contamination in wildlife? Combining stable isotopes and GPS tracking in three gull species.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {391},
number = {},
pages = {127556},
doi = {10.1016/j.envpol.2025.127556},
pmid = {41419039},
issn = {1873-6424},
mesh = {Animals ; *Charadriiformes/metabolism ; *Fluorocarbons/metabolism/blood ; *Ecosystem ; *Environmental Monitoring/methods ; France ; Geographic Information Systems ; Male ; *Environmental Pollutants/metabolism/blood ; Female ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; Food Chain ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) are toxic and persistent compounds widely distributed in the environment and accumulate in top predators, including seabirds. Because of the biomagnification potentials of some PFAS, diet is thought to be a key exposure route for PFAS. However, other factors such as habitat use, may mask interspecific differences in PFAS exposure expected from trophic structure. Among seabirds, gulls are generalists that forage in both terrestrial and marine habitats, making them relevant models to concurrently investigate the influence of foraging habitats and trophic position on PFAS exposure. We combined plasma PFAS concentrations with GPS tracking and stable isotopes to define foraging habitats (δ[13]C; δ[34]S; GPS) and trophic positions (δ[15]N) in three sympatric gull species breeding in France (Isle of Ré). In herring gulls (Larus argentatus), long-chain perfluoroalkyl carboxylic acids (PFCAs) were positively correlated with high trophic resources from marine habitats. We found compound- and sex-dependent relationships between PFAS concentrations and stable isotope values in lesser black-backed gulls (Larus fuscus), while no association was found with habitat use. No association was found between PFAS levels and stable isotopes in great black-backed gulls (Larus marinus). Our study suggests that coastal habitat could be a source of PFCA contamination and highlights that the influence of habitat use on gull exposure to PFAS varied depending on species, sex, and compounds.},
}

Animals
*Charadriiformes/metabolism
*Fluorocarbons/metabolism/blood
*Ecosystem
*Environmental Monitoring/methods
France
Geographic Information Systems
Male
*Environmental Pollutants/metabolism/blood
Female
Carbon Isotopes/analysis
Nitrogen Isotopes/analysis
Food Chain

@article {pmid41352621,
year = {2026},
author = {Kissane, ZM and Warren, KS and Yeap, L and Shephard, JM},
title = {Hazard identification and ecological risk assessment of pesticide exposure in wildlife using GPS telemetry: Case study on endangered Carnaby's Cockatoos.},
journal = {Environmental toxicology and pharmacology},
volume = {121},
number = {},
pages = {104894},
doi = {10.1016/j.etap.2025.104894},
pmid = {41352621},
issn = {1872-7077},
mesh = {Animals ; Risk Assessment ; Endangered Species ; *Pesticides/toxicity/analysis ; Telemetry ; Environmental Monitoring/methods ; Geographic Information Systems ; *Environmental Exposure/analysis ; Animals, Wild ; *Environmental Pollutants/analysis/toxicity ; },
abstract = {Wildlife toxicology faces increasing threats from pesticide use, yet the impacts on biodiversity remain unclear, as current toxicity thresholds often rely on laboratory data that do not reflect environmental exposure. Here we present a two-step methodology integrating ecotoxicology and movement ecology to investigate pesticide exposure in endangered Carnaby's cockatoos (Zanda latirostris). Using GPS telemetry and satellite tracking, this study identified pesticide exposure sites and quantified the likelihood and consequences of exposure. A total of 26 pesticides were detected in forage sources (agricultural seed), with 80 % of seed samples having one or more pesticides detected. The Maximum Residue Limit (MRL) was exceeded for multiple pesticides including imidacloprid, thiamethoxam, clothianidin, difenoconazole and metalaxyl. Results have highlighted the risks that granivorous birds face being exposed to insecticides, herbicides, and fungicides in agroecosystems. This methodology is broad in scope and applicable across species, providing the ecological realism missing in laboratory-based studies.},
}

Animals
Risk Assessment
Endangered Species
*Pesticides/toxicity/analysis
Telemetry
Environmental Monitoring/methods
Geographic Information Systems
*Environmental Exposure/analysis
Animals, Wild
*Environmental Pollutants/analysis/toxicity

@article {pmid41512112,
year = {2026},
author = {Shimmura, T and Kurachi, T and Matsuda, Y and Rafati, N and Shimura, K and Goto, T and Kawakami, SI and Maeda, R and Yamada, Y and Pettersson, ME and Nakamura, Y and Higashiura, Y and Shimura, NN and Bendesky, A and Tsudzuki, M and Andersson, L},
title = {Genomic and neurobiological bases of variation in fighting strategies in gamecocks.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag007},
pmid = {41512112},
issn = {1537-1719},
abstract = {Aggression is an essential animal behavior for survival, particularly in situations where fighting cannot be avoided. In such situations, the choice of fighting strategy (e.g., biting, charging, or defending) is critical. Although molecular bases of fighting and aggressiveness have been previously studied, how genetic, transcriptional, and neurobiological mechanisms contribute to the choice of fighting strategy remains largely unknown. Here, we use two subpopulations of chickens bred for cockfighting that show markedly different fighting strategies: offensive and defensive attack. A genome-wide screen comparing individuals from the two subpopulations indicated a polygenic background and we identified 15 candidate genes, five of which are implicated in neuronal development. Among these, the transcription factor gene FOXP1 was notable. FOXP1 is essential for neuronal development in the brain and has been implicated in the regulation of motor circuits. Transcriptomic analysis of the diencephalon also revealed differential expressions of genes involved in neurodevelopment, as well as in the synthesis and release of neurotransmitters. RNA-sequencing and immunohistochemistry suggested that activation of the indirect pathway of the brain motor circuit promotes the defensive fighting strategy. This was further supported by behavioral pharmacological experiments targeting dopaminergic signaling. Taken together, our results indicate that genomic variation and altered expression of neurodevelopment-related genes underlie differences in fighting strategies, and that the neuroendocrine changes in brain circuits further modulate these behavioral outcomes.},
}

@article {pmid41506426,
year = {2026},
author = {Geng, Y and Guo, W and Li, Q and Zhang, F and Zhong, A and Hu, Z},
title = {Driving Mechanisms of Vegetation Carbon Sink Distribution Based on Explainable Machine Learning and Evaluation of Carbon Sequestration in Open-Pit Mines.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123715},
doi = {10.1016/j.envres.2026.123715},
pmid = {41506426},
issn = {1096-0953},
abstract = {Vegetation carbon sequestration plays a crucial role in mitigating global warming and maintaining regional carbon balance. The Yellow River Basin (YRB) is a key region for energy development and ecological conservation in China, yet the driving mechanisms underlying the spatial distribution of vegetation carbon sequestration and the carbon sequestration capacity of open-pit mines have not been systematically evaluated. Based on multi-source datasets, this study first employs the Sen's slope estimator combined with the Mann-Kendall trend test model to identify the temporal trends of vegetation carbon sequestration. It then applies a Bayesian-optimized Bayesian-optimized Extreme Gradient Boosting model integrated with Shapley Additive Explanations model to uncover the driving mechanisms of climate, soil, and human activities on its spatial distribution. Finally, a buffer zone comparison method is used to quantify the carbon sequestration potential of open-pit mines. The main conclusions are as follows: (1) Over the 24-year period, Net Ecosystem Productivity (NEP) in the YRB has shown a continuous increase, reaching 159.69 gC·m[-2] in 2024, which is five times the level in 2001. The most significant growth occurred in the middle and upper reaches, while the endorheic region exhibited limited improvement, with some areas even functioning as carbon sources. (2) Among the driving factors of NEP distribution in the YRB, precipitation, solar radiation, and soil organic carbon are the dominant contributors, accounting for more than 58% in total. (3) The NEP of different types of open-pit mines varies substantially. Active mines function overall as carbon sources (-17.93 Gg), whereas stable and revegetated mines act as carbon sinks. The total carbon sequestration potential of all open-pit mines is 93.57 Gg, representing approximately 89% of the current carbon sequestration level. This study provides a quantitative foundation for enhancing carbon sequestration, evaluating ecological restoration, and supporting the implementation of the "dual-carbon" strategy in the YRB.},
}

@article {pmid41503483,
year = {2026},
author = {Castillo-Neyra, R and Ortiz-Cam, L and Díaz, EW and Cañari-Casaño, JL and Recuenco, SE and Paz-Soldán, VA},
title = {The return of human rabies: A foretold case in Latin America Through the Lens of One Health.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {41503483},
abstract = {BACKGROUND: Despite ongoing rabies control efforts in Arequipa, Peru-including mass dog vaccination campaigns and reactive ring interventions-the region has failed to reduce the number of rabid dogs, leading to the first reported human dog-mediated rabies case after 8 years. The gaps in the rabies control program and the complex dynamics among stakeholders are unknown.

OBJECTIVE: To integrate epidemiologic, socio-ecological, and policy data to identify the factors contributing to the 2023 human rabies case and propose strategies to make this a 'never event'.

METHODS: We used stakeholder mapping and field quantitative and qualitative data to identify the roles and connections of key actors in rabies control, identifying gaps in their functions. We then applied the Swiss Cheese model to characterize the defense layers against dog-mediated rabies, highlighting critical vulnerabilities across these protective barriers.

CONCLUSIONS: We identified multiple breaches in the defense against dog-mediated human rabies. Weak surveillance, insufficient dog vaccination, and inadequate management of free-roaming and feral dogs, coupled with bureaucratic inefficiencies, were key gaps. Outbreak responses were delayed and insufficient, and access to post-exposure prophylaxis (PEP) remained limited. Communication breakdowns exacerbated the problem. Systemic issues, such as outdated public health policies, insufficient training of health professionals, and fragmented efforts, further hindered timely exposure response. Dog ecology and demographic factors also contributed to dog rabies spread. These failures in policy, response, capacity, and external factors led to the 2023 human rabies case. Despite awareness of these challenges, the contributing conditions remain unchanged. Eliminating dog-mediated human rabies by 2030 will require targeted interventions, including enhanced surveillance, context-specific policy reforms, stronger community and institutional collaboration, and better management of free-roaming dogs.},
}

@article {pmid41360908,
year = {2025},
author = {Huang, Y and Han, X and Xia, C},
title = {Assessing the completeness and consistency of global-scale avian datasets.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1201},
pmid = {41360908},
issn = {2045-2322},
support = {32170491//National Natural Science Foundation of China/ ; },
mesh = {*Birds/physiology/classification ; Animals ; Ecosystem ; *Databases, Factual ; Biodiversity ; Ecology ; },
abstract = {The advancement of ecological research has increasingly focused on comparative methods and global-scale analyses. Birds are frequently selected for such studies for their widespread distribution and sensitivity to environmental changes. Given the need to integrate fragmented avian data, we aim to collect global-scale avian datasets and evaluate the completeness and consistency of them. We reviewed literature published in Springer Nature and American Association for the Advancement of Science (AAAS) from 2020 to 2024 and identified 90 articles with large-scale coverage and broad taxonomic representation. From these, we compiled 123 datasets covering environmental factors, avian traits, and ecosystem-level data. These were categorized into species-level and spatial data for completeness assessment, while consistency was evaluated across three modalities: species lists, nominal variables, and continuous variables. The database encompassed 12 distinct data types, including morphological, physiological, behavioural, and life-history traits, niche characteristics, evolutionary data, and environmental factors. Our assessment revealed that species distribution and abundance data were most frequently utilized in avian research worldwide. Both the species-level and spatial data exhibited high completeness. Continuous variables showed high consistency, whereas nominal variables and species lists exhibited moderate consistency with notable variability. Therefore, the supplementation of low-integrity data such as reproductive and behavioural datasets remains imperative. Systematic reconciliation between legacy and revised avian taxonomic inventories are critical for ensuring the consistency of data. We hope that the work can advance understanding of macroecology and providing guidance for global avian research.},
}

*Birds/physiology/classification
Animals
Ecosystem
*Databases, Factual
Biodiversity
Ecology

@article {pmid40491419,
year = {2026},
author = {Tuerlinckx, F and Kuppens, P and Ariens, S and Cloos, L and Dejonckheere, E and Lafit, G and Niemeijer, K and Revol, J and Schat, E and Schreuder, M and Vanhasbroeck, N and Ceulemans, E},
title = {New developments in experience sampling methodology.},
journal = {The British journal of mathematical and statistical psychology},
volume = {79},
number = {1},
pages = {46-65},
doi = {10.1111/bmsp.12398},
pmid = {40491419},
issn = {2044-8317},
support = {//Fonds Wetenschappelijk Onderzoek/ ; //Onderzoeksraad, KU Leuven/ ; C14/23/062//KU Leuven Research Council/ ; IBOF/21/090//IBOF/ ; EOS 4000528/G0I2422N//EOS excellence of science program/ ; },
mesh = {Humans ; Reproducibility of Results ; *Research Design ; Data Interpretation, Statistical ; *Ecological Momentary Assessment/statistics & numerical data ; Models, Statistical ; Self Report ; Sample Size ; Smartphone ; },
abstract = {Experience Sampling Methodology (ESM) has been widely used over the past decades to study feelings, behaviour and thoughts as they occur in daily life. Typically, participants complete several assessments per day via a smartphone for multiple days. The growing adoption of ESM has spurred a number of methodological advancements. In this paper, we provide an overview of recent developments in ESM design, statistical analysis and implementation. In terms of design, we discuss considerations around what to measure-including the reliability and validity of self-report measures as well as mobile sensing-as well as when to measure, where we focus on the pros and cons of burst designs and advances in sample size planning methodology. Regarding statistical analysis, we highlight non-linear models, survival analysis for understanding time-to-event data and real-time monitoring of ESM time series. At the implementation level, we address open science practices and advances in data preprocessing. Although most of the topics discussed in this paper are generic, many of the examples are focused on the study of affect in daily life.},
}

Humans
Reproducibility of Results
*Research Design
Data Interpretation, Statistical
*Ecological Momentary Assessment/statistics & numerical data
Models, Statistical
Self Report
Sample Size
Smartphone

@article {pmid41499681,
year = {2026},
author = {Astill Wright, L and Shajan, G and Purewal, D and Stone, J and Majid, M and Guo, B and Morriss, R},
title = {Mood Monitoring, Mood Tracking, and Ambulatory Assessment Interventions in Depression and Bipolar Disorder: Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {JMIR mental health},
volume = {13},
number = {},
pages = {e84020},
pmid = {41499681},
issn = {2368-7959},
mesh = {Humans ; *Bipolar Disorder/therapy/diagnosis/psychology ; Randomized Controlled Trials as Topic ; *Affect ; *Monitoring, Ambulatory/methods ; *Depressive Disorder/therapy/diagnosis ; *Depression/diagnosis/therapy ; },
abstract = {BACKGROUND: Mood monitoring is widely used by people with depression and bipolar disorder (BD) to prevent relapse and improve insight into their condition, but it is unclear if these interventions have an impact on symptoms and for whom. As the capacity for passive mood monitoring increases, it is vital to improve our understanding of frequent mood assessment.

OBJECTIVE: This systematic review and meta-analysis assessed the effect of mood monitoring interventions in people with depression and BD to decrease relapse risk and symptoms of depression and mania.

METHODS: We conducted a systematic review and meta-analysis (PROSPERO, International Prospective Register of Systematic Reviews: CRD42023396473) and reported results according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. Randomized controlled trials with clinically important follow-up periods were identified via multiple database searches and rated for risk of bias using the Cochrane Risk of Bias tool. The primary outcomes were symptoms of depression and mania. Available data were pooled to calculate standardized mean differences (SMDs) for the primary outcomes: severity of depression, bipolar depression, and mania/hypomania.

RESULTS: We included 8 trials of 1230 participants and 6 different mood monitoring protocols. In BD, meta-analysis found a small but not statistically significant effect of mood monitoring interventions on decreasing mania symptoms (6 comparisons, n=873; SMD 0.16, 95% CI-0.34 to 0.01; P=.06) and no effect on bipolar depression (6 comparisons, n=873; SMD -0.08, 95% CI -0.31 to 0.15; P=.02). In depression, we found a small effect in decreasing symptoms of depression of borderline statistical significance at 12 months (2 comparisons, n=262; SMD -0.25, 95% CI -0.49 to 0.00; P=.05) but not at 6 months (2 comparisons, n=268; SMD -0.21, 95% CI -0.54 to 0.12; P=.21). There was an absence of evidence on the effect of mood monitoring on decreased relapse rates or readmission rates. Studies had a low risk of bias. There was no evidence on mood monitoring through ecological momentary assessment.

CONCLUSIONS: Overall mood monitoring interventions do not increase or decrease mood symptoms in people with BD, nor is there robust evidence of such effects in people with unipolar depression. Further research is merited on different forms of mood monitoring and to determine under what circumstances mood monitoring might have beneficial or adverse effects. These results initially suggest that ambulatory assessment does not induce large placebo effects or significantly negatively or positively affect mood, and thus that mood monitoring may be an appropriate outcome measure for research or for clinical practice.},
}

Humans
*Bipolar Disorder/therapy/diagnosis/psychology
Randomized Controlled Trials as Topic
*Affect
*Monitoring, Ambulatory/methods
*Depressive Disorder/therapy/diagnosis
*Depression/diagnosis/therapy

@article {pmid41502546,
year = {2025},
author = {Boyes, D and Hutchinson, F and Crowley, LM and , and , and , and , and , and , and , },
title = {The genome sequence of the Red-barred Tortrix moth, Ditula angustiorana (Haworth, 1811).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {202},
doi = {10.12688/wellcomeopenres.23994.1},
pmid = {41502546},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Ditula angustiorana (Red-barred Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 468.36 megabases. Most of the assembly (99.83%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 16.19 kilobases.},
}

@article {pmid41502542,
year = {2025},
author = {Crowley, LM and Hutchinson, F and Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Barred Hook-tip, Watsonalla cultraria (Fabricius, 1775) (Lepidoptera: Drepanidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {618},
doi = {10.12688/wellcomeopenres.25058.1},
pmid = {41502542},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Watsonalla cultraria (Barred Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence has a total length of 319.38 megabases. Most of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Gene annotation of this assembly on Ensembl identified 16 011 protein-coding genes. The mitochondrial genome has also been assembled, with a length of 15.21 kilobases.},
}

@article {pmid41502538,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Drinker, Euthrix potatoria (Linnaeus, 1758) (Lepidoptera: Lasiocampidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {534},
doi = {10.12688/wellcomeopenres.24922.1},
pmid = {41502538},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Euthrix potatoria (Drinker; Arthropoda; Insecta; Lepidoptera; Lasiocampidae). The assembly contains two haplotypes with total lengths of 487.86 megabases and 466.06 megabases. Most of haplotype 1 (99.97%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 15.43 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41501044,
year = {2026},
author = {von Borries, K and Beckwith, KV and Goodman, JM and Chiu, WA and Jolliet, O and Fantke, P},
title = {Uncertainty-aware machine learning to predict non-cancer human toxicity for the global chemicals market.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67374-4},
pmid = {41501044},
issn = {2041-1723},
support = {DIA 2018/11//Stiftelsen för Miljöstrategisk Forskning (Swedish Foundation for Strategic Environmental Research)/ ; DIA 2018/11//Stiftelsen för Miljöstrategisk Forskning (Swedish Foundation for Strategic Environmental Research)/ ; DIA 2018/11//Stiftelsen för Miljöstrategisk Forskning (Swedish Foundation for Strategic Environmental Research)/ ; EP/S024220/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; P30 ES029067/ES/NIEHS NIH HHS/United States ; P42 ES027704/ES/NIEHS NIH HHS/United States ; },
abstract = {Humans are exposed to thousands of chemicals, yet limited toxicity data hinder effective management of their impacts on human health. High-performing machine learning models hold potential for addressing this gap, but their uncharacterized prediction performance across the wider range of chemicals undermines confidence in their results. We develop uncertainty-aware models to predict reproductive/developmental and general non-cancer human toxicity effect doses. Our well-calibrated models provide uncertainty estimates aligned with observed prediction errors and chemical familiarity. We predict toxicity with 95% confidence intervals for >100,000 globally marketed chemicals and identify toxicity and uncertainty hotspots. These results can be applied to inform decisions aimed at reducing potential human health impacts and guide targeted data generation and modeling efforts to reduce prediction uncertainty. Here, we show that enhancing transparency in prediction uncertainty provides key insights for building confidence in toxicity predictions, supporting the sound integration of machine learning-based predictions in chemical assessments.},
}

@article {pmid41497383,
year = {2025},
author = {Hostens, M and Franceschini, S and van Leerdam, M and Yang, H and Pokharel, S and Liu, E and Niu, P and Zhang, H and Noor, S and Hermans, K and Salamone, M and Sharma, S},
title = {The future of big data and artificial intelligence on dairy farms: A proposed dairy data ecosystem.},
journal = {JDS communications},
volume = {6},
number = {Suppl 1},
pages = {S9-S14},
pmid = {41497383},
issn = {2666-9102},
abstract = {The dairy sector should overcome challenges in productivity, sustainability, and data management by adopting intelligent, scalable, and privacy-preserving technological solutions. Adopting data and artificial intelligence (AI) technologies is essential to ensure efficient operations and informed decision making and to keep a competitive market advantage. This paper proposes an integrated, multimodal AI framework to support data-intensive dairy farm operations by leveraging big data principles and advancing them through AI technologies. The proposed architecture incorporates edge computing, autonomous AI agents, and federated learning to enable real-time, privacy-preserving analytics at the farm level and promote knowledge sharing and refinement through research farms and cloud collaboration. Farms collect heterogeneous data, which can be transformed into embeddings for both local inference and cloud analysis. These embeddings form the input of AI agents that support health monitoring, risk prediction, operational optimization, and decision making. Privacy is preserved by sharing only model weights or anonymized data externally. The edge layer handles time-sensitive tasks and communicates with a centralized enterprise cloud hosting global models and distributing updates. A research and development cloud linked to research farms ensures model testing and validation. The entire system is orchestrated by autonomous AI agents that manage data, choose models, and interact with stakeholders, and human oversight ensures safe decisions, as illustrated in the practical use case of mastitis management. This architecture could support data integrity, scalability, and real-time personalization, along with opening up space for partnerships between farms, research institutions, and regulatory bodies to promote secure, cross-sector innovation.},
}

@article {pmid41494263,
year = {2026},
author = {Mummidivarapu, SK and Rehana, S},
title = {Spatiotemporal risk assessment of river water quality for tropical river systems using hydrological dynamics, anthropogenic influences, and ecological health index.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181329},
doi = {10.1016/j.scitotenv.2025.181329},
pmid = {41494263},
issn = {1879-1026},
abstract = {Sustainable management of River Water Quality (RWQ) in tropical river systems requires an approach that addresses both spatial and temporal risks associated with hydrological dynamics, anthropogenic influences, and ecological health. This study develops an uncertainty-aware spatiotemporal risk assessment approach integrating upstream hydrological dynamics (SWAT), operational variability with Environmental Flow (Eflow), water quality simulations (QUAL2K), and probabilistic Water Quality Index (WQI) calculations. Block-Bootstrap ensembles and Monte Carlo techniques are used to quantify uncertainty propagation and construct confidence intervals within the model chain. The monthly WQI estimates under the different Eflow and pollution control scenarios are used to assess the spatial risk variability of the river system. Temporal risk was assessed with WQI using various probabilistic measures, including mean, variance, loss probability, entropy, mean excess loss, and value at risk. A unified risk ranking was developed by using Borda and Copeland aggregation techniques. Categorised spatial risk maps were created using GIS by integrating Eflows and ecological index. The results revealed significant seasonal variations in water quality, with April, March, and May identified as high-risk months due to increased pollution levels. The monthly WQI-mean in the Monte Carlo analysis (1000 iterations), as per the severity of the risk, April, March, and May months are identified as the riskiest months. Spatial risk mapping revealed distinct high-risk zones and highlighted the necessity of pollution treatment level of 25-50 % to reduce ecological risk under optimal Eflow regimes. This comprehensive framework underscores the need for both flow regulation and pollution management to protect river ecosystems, providing actionable insights for effective river health protection.},
}

@article {pmid41480146,
year = {2025},
author = {Formenti, G and Jain, N and Medico, JA and Sollitto, M and Antipov, D and Barcellos, S and Biegler, M and Borges, I and Chang, JK and Chen, Y and Cheng, H and Conceição, H and Davenport, M and De Oliveira, L and Duarte, E and Durham, G and Fenn, J and Forde, N and Galante, PA and Gerhardt, K and Giani, AM and Giunta, S and Kim, J and Komissarov, A and Koo, B and Koren, S and Larkin, D and Lee, C and Li, H and Makova, K and Masterson, P and Murphy, T and McCaffrey, K and Mercuri, RLV and Na, Y and O'Connell, MJ and Ou, S and Phillippy, A and Popova, M and Rhie, A and Ruiz-Ruano, FJ and Secomandi, S and Smeds, L and Suh, A and Tilley, T and Vontzou, N and Waters, PD and Balacco, J and Jarvis, ED},
title = {The complete genome of a songbird.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41480146},
issn = {2692-8205},
abstract = {Bird genomes are the smallest among amniotes, but remain challenging to assemble due to their structural complexity. This study presents the first fully phased, diploid, telomere-to-telomere (T2T) reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining multiple sequencing strategies resulted in closing nearly all gaps, adding ~90 Mbp of previously missing sequence (7.8%). This includes T2T assemblies for all microchromosomes, including dot chromosomes, and the previously almost entirely missing chr16. The T2T genome is comprehensively annotated for genes, repeats, structural variants, and long-read methylation calls. Complete centromeric structures were assembled and annotated along with kinetochore binding sites. Relative to the previous high-quality reference of the Vertebrate Genomes Project, 2,778 (8.51%) previously unassembled or unannotated genes were identified, of which 9% overlap with segmental duplications. This first complete genome of a songbird, now the new public reference, illuminates avian genome architecture and function.},
}

@article {pmid41399279,
year = {2026},
author = {Culina, A},
title = {Co-BreeD: A milestone resource for studies on cooperative breeding.},
journal = {The Journal of animal ecology},
volume = {95},
number = {1},
pages = {17-20},
doi = {10.1111/1365-2656.70205},
pmid = {41399279},
issn = {1365-2656},
support = {HRZZ-IP-2022-10-2872//Hrvatska Zaklada za Znanost/ ; },
mesh = {Animals ; *Cooperative Behavior ; *Breeding ; *Databases, Factual ; *Birds/physiology ; *Mammals/physiology ; *Reproduction ; },
abstract = {Research Highlight: Ben Mocha, Y., Woith, M., Scemama de Gialluly, S., Bruscagnin, L., Kestel, N., Markman, S., Drobniak, S. M., Baglione, V., Boersma, J., Cousseau, L., Covas, R., Braga de Miranda, G. H., Dey, C. J., Doutrelant, C., Gula, R., Heinsohn, R., Keynan, O., Kingma, S. A., Leitão, A. V., … Griesser, M. (2025). An integrative, peer-reviewed open-source cooperative-breeding database (Co-BreeD). Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.70154. The Cooperative-Breeding Database (Co-BreeD) is an open, peer-reviewed resource that collects data on cooperative breeding across birds and mammals, including humans. As such, it serves as a valuable resource for studies on sociality and cooperation. Currently, Co-BreeD provides population-level data on nearly 40,000 breeding events from 316 species and is growing. The database allows for cooperative breeding to be treated as a continuous rather than binary trait, and at finer spatial and temporal scales, enabling detailed exploration of the ecological and evolutionary drivers of cooperation. This novel approach revealed that alloparental care, and hence cooperative breeding, is likely more widespread than previously recognised. The importance of curated, high-quality, and accessible data across ecology and evolution is becoming evident; Co-BreeD has great potential to contribute to such collaborative, reproducible, and robust research.},
}

Animals
*Cooperative Behavior
*Breeding
*Databases, Factual
*Birds/physiology
*Mammals/physiology
*Reproduction

@article {pmid41492055,
year = {2026},
author = {Marinucci, M and Schaefer, CD and Dupont, PL and Manley, D and Taylor, LK and McKeown Jones, S},
title = {Desegregating spaces: The interplay between ecological intergroup contact and GPS-traced spatial segregation among youth in two UK cities.},
journal = {The British journal of social psychology},
volume = {65},
number = {1},
pages = {e70043},
doi = {10.1111/bjso.70043},
pmid = {41492055},
issn = {2044-8309},
support = {//Economic and Social Research Council/ ; },
mesh = {Humans ; Adolescent ; Male ; Female ; Geographic Information Systems ; United Kingdom ; *Social Segregation/psychology ; Cities ; Ecological Momentary Assessment ; Ethnicity/psychology ; *Group Processes ; *Interpersonal Relations ; },
abstract = {Recent advances in intergroup contact research have drawn on methods from human geography to investigate how segregation shapes, and is shaped by, everyday intergroup experiences. Emerging findings suggest that the phenomena might be reciprocally intertwined, but empirical evidence is limited and mixed. This research tested the reciprocal relationship between everyday intergroup contact and segregation using ecological momentary assessment and GPS-GIS tracking in two segregated UK cities with youths aged 15-17. Study 1 (Belfast; nparticipants = 15; ninteractions = 115; nGPS-point = 633) focused on Catholics-Protestants divisions, and Study 2 (Bradford; nparticipants = 30; ninteractions = 334; nGPS-point = 2868) addressed ethnic segregation among Asian, White, and Black communities. In both studies, youths reported on social interactions throughout 6 days, while their urban mobility in outgroup spaces was tracked. In Belfast, more mixed districts predicted higher anxiety during intergroup interactions, yet, positive intergroup contact was followed by increased visits to outgroup spaces. In Bradford, mixed districts increased the likelihood (but not the quality) of intergroup contact, while the link between positive contact and subsequent outgroup space use was replicated. The findings highlight a virtuous cycle depending on contextual norms by which positive contact and desegregation practices might reinforce each other, arguably demonstrating the potential of intergroup contact for levelling urban divisions.},
}

Humans
Adolescent
Male
Female
Geographic Information Systems
United Kingdom
*Social Segregation/psychology
Cities
Ecological Momentary Assessment
Ethnicity/psychology
*Group Processes
*Interpersonal Relations

@article {pmid41491638,
year = {2026},
author = {Wang, Y and Zhao, J and He, X and Yang, D and Jin, Y and Wu, R},
title = {A Computational Ecological Genetic Model of Phenotypic Plasticity in Species Interactions.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70095},
doi = {10.1111/1755-0998.70095},
pmid = {41491638},
issn = {1755-0998},
support = {SIMIS-ID-2024-WN//Interdisciplinary Project at Shanghai Institute for Mathematics and Interdisciplinary Sciences/ ; 31971398//National Natural Science Foundation of China/ ; },
mesh = {Phenotype ; *Escherichia coli/genetics/physiology/growth & development ; *Staphylococcus aureus/genetics/physiology/growth & development ; *Models, Genetic ; *Computational Biology/methods ; Genotype ; *Microbial Interactions ; Epistasis, Genetic ; },
abstract = {Multiple species respond to each other in their co-existing communities. Such reciprocal phenotypic plasticity can shape the behaviour and evolution of ecological communities, but its genetic architecture remains elusive. We address this issue by developing a computational mapping model that combines community ecology and quantitative genetics into a unifying context. Culturing a pair of genotypes from two species in a socially isolated environment (monoculture) and a socialised environment (co-culture) allows for the quantitative estimation of reciprocal phenotypic plasticity, that is, the difference between trait values of one (defensive) species expressed in the monoculture and the co-culture with the other (offensive) species. Classic quantitative genetic theory is implemented to map genetic variants for reciprocal phenotypic plasticity, including defensive loci derived from the defensive species and offensive loci from the offensive species, and estimate the direct effects of the defensive loci, the indirect effects of the offensive loci and horizontal epistasis due to interactions between the two genomes. We design an ecological genetic experiment of monocultures and co-cultures using 100 pairs of genotyped Escherichia coli and Staphylococcus aureus strains, from which the model identifies the existence of defensive and offensive loci, despite a remarkable asymmetry between the two bacterial species. We find that horizontal epistasis between defensive and offensive loci plays a sizable role in mediating reciprocal phenotypic plasticity. The biological functions of these identified loci are annotated via GO analysis. Our model could produce unique results that shed light on the genetic mechanisms of interspecies interactions and their adaptation in ecological communities.},
}

Phenotype
*Escherichia coli/genetics/physiology/growth & development
*Staphylococcus aureus/genetics/physiology/growth & development
*Models, Genetic
*Computational Biology/methods
Genotype
*Microbial Interactions
Epistasis, Genetic

@article {pmid41488783,
year = {2026},
author = {Luongo, G and Dell'Anno, A and Tangherlini, M and Corinaldesi, C and A Ruhl, H and Danovaro, R},
title = {Major changes in micro-eukaryotic biodiversity of the abyssal ecosystem of the NE Atlantic: A comparison between 1996 and 2018.},
journal = {iScience},
volume = {29},
number = {1},
pages = {114266},
pmid = {41488783},
issn = {2589-0042},
abstract = {Time-separated snapshots of deep-sea regions can provide crucial insights into how fluctuations in environmental changes and food supply shape microbial communities. Here, we compared molecular and environmental data collected in 1996 and 2018 at 4,800-m depth in the northeast (NE) Atlantic Ocean. We report lower values of primary production (-66%) associated with lower concentrations of sedimentary labile organic matter (-12%). Metabarcoding analyses revealed a significant decrease in the Chlorophyta taxa, only partly compensated by the increase in Dinoflagellate taxa, consistent with patterns observed in NE Atlantic Ocean phytoplankton. Benthic prokaryotic assemblages showed a limited response to such changes, whilst micro-eukaryotic assemblages changed significantly even at subdivision level. Overall, data reported here suggest that the Porcupine abyssal plain may undergo significant variations in terms of quantity and quality of biopolymeric carbon and that such changes caused a shift in micro-eukaryotic biodiversity, with potentially relevant effects also on the deep-sea ecosystem functioning.},
}

@article {pmid41460880,
year = {2025},
author = {Langmüller, AM and Chandrasekher, KA and Haller, BC and Champer, SE and Murdock, CC and Messer, PW},
title = {Gaussian process emulation for exploring complex infectious disease models.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013849},
doi = {10.1371/journal.pcbi.1013849},
pmid = {41460880},
issn = {1553-7358},
mesh = {Humans ; Normal Distribution ; Dengue/epidemiology ; *Communicable Diseases/epidemiology ; *Epidemiological Models ; Computational Biology ; Disease Outbreaks/statistics & numerical data ; Colombia/epidemiology ; Computer Simulation ; Epidemics/statistics & numerical data ; Seasons ; Models, Statistical ; },
abstract = {Epidemiological models that aim for a high degree of biological realism by simulating every individual in a population are unavoidably complex, with many free parameters, which makes systematic explorations of their dynamics computationally challenging. In this study, we demonstrate how Gaussian Process emulation can overcome this challenge. To simulate disease dynamics, we developed an abstract individual-based model that is loosely inspired by dengue, incorporating some key features shaping dengue epidemics such as social structure, human movement, and seasonality. We focused on three epidemiological metrics derived from the individual-based model outcomes - outbreak probability, maximum incidence, and epidemic duration - and trained three Gaussian Process surrogate models to approximate these metrics. The GP surrogate models enabled the rapid prediction of these epidemiological metrics at any point in the eight-dimensional parameter space of the original model. Our analysis revealed that average infectivity and average human mobility are key drivers of these epidemiological metrics, while the seasonal timing of the first infection can influence the course of the epidemic outbreak. We used a dataset comprising more than 1,000 dengue epidemics observed over 12 years in Colombia to calibrate our Gaussian Process model and evaluated its predictive power. The calibrated Gaussian Process model identified a subset of municipalities with consistently higher average infectivity estimates; the notable overlap between these municipalities and previously reported dengue disease clusters suggests that statistical emulation can facilitate empirical data analysis. Overall, this work underscores the potential of Gaussian Process emulation to enable the use of more complex individual-based models in epidemiology, allowing a higher degree of realism and accuracy that should increase our ability to control diseases of public health concern.},
}

Humans
Normal Distribution
Dengue/epidemiology
*Communicable Diseases/epidemiology
*Epidemiological Models
Computational Biology
Disease Outbreaks/statistics & numerical data
Colombia/epidemiology
Computer Simulation
Epidemics/statistics & numerical data
Seasons
Models, Statistical

@article {pmid41178269,
year = {2026},
author = {Ono, S and Takebe, K and Tosa, I and Nishiya, Y and Nakayama, M and Wada, T and Takashiba, S and Ohara, N},
title = {PGN_0298 in the Assembly and Insertion Machinery (Aim) Operon Is Essential for the Viability of Porphyromonas gingivalis.},
journal = {Microbiology and immunology},
volume = {70},
number = {1},
pages = {9-14},
doi = {10.1111/1348-0421.70021},
pmid = {41178269},
issn = {1348-0421},
support = {//JSPS KAKENHI Grant Number JP24K02614 (NO), JP23K15970 (SO), JP21K09842 (MN), JP24K23551 (KT)./ ; },
mesh = {*Porphyromonas gingivalis/genetics/physiology ; *Operon ; Gingipain Cysteine Endopeptidases ; Virulence Factors/genetics/metabolism ; Adhesins, Bacterial/metabolism/genetics ; Cysteine Endopeptidases/metabolism/genetics ; *Microbial Viability ; *Bacterial Proteins/genetics/metabolism ; Computational Biology ; Humans ; Bacterial Secretion Systems/genetics ; },
abstract = {Porphyromonas gingivalis is a typical periodontal pathogen, and one of its key virulence factors is the powerful protease gingipains. Gingipains are secreted via the type IX secretion system (T9SS) and are associated with the assembly and insertion machinery (Aim) operon (PGN_0296 to PGN_0301), which encodes both T9SS components and non-T9SS proteins. In this study, we investigated PGN_0298, a gene of unknown function within this operon, to elucidate its role in P. gingivalis and to gain insights into its potential function through bioinformatics analyses. Our results demonstrated that PGN_0298 is essential for the viability of P. gingivalis, despite having limited direct association with T9SS. Sequence homology and structure predictions indicate that PGN_0298 encodes a putative isoprenyl transferase. The essentiality of PGN_0298 underscores its potential as a novel drug target for the treatment of periodontal disease.},
}

*Porphyromonas gingivalis/genetics/physiology
*Operon
Gingipain Cysteine Endopeptidases
Virulence Factors/genetics/metabolism
Adhesins, Bacterial/metabolism/genetics
Cysteine Endopeptidases/metabolism/genetics
*Microbial Viability
*Bacterial Proteins/genetics/metabolism
Computational Biology
Humans
Bacterial Secretion Systems/genetics

@article {pmid40833038,
year = {2026},
author = {De Neef, E and Velásquez-Zapata, V and Gordon, ERL and Narva, K and Mc Cahon, P and Mézin, L and Lester, PJ and Romeis, J and Fletcher, S and Mitter, N and Devisetty, UK and Sridharan, K},
title = {A bioinformatic ecological risk assessment framework for externally applied double-stranded RNA-based biopesticides.},
journal = {Integrated environmental assessment and management},
volume = {22},
number = {1},
pages = {116-131},
doi = {10.1093/inteam/vjaf116},
pmid = {40833038},
issn = {1551-3793},
mesh = {*RNA, Double-Stranded/toxicity ; Risk Assessment/methods ; *Computational Biology/methods ; *Biological Control Agents/toxicity ; *Pest Control, Biological/methods ; Animals ; *Pesticides/toxicity ; },
abstract = {Double-stranded RNA (dsRNA)-based biopesticides are a promising new method of pest management. These biopesticides leverage the endogenous RNA interference pathway to selectively regulate expression of key genes involved in growth and development in pests, providing the potential to minimize harmful environmental effects by highly specific targeting. As dsRNA-based biopesticides are presented for regulatory review, evaluating potential off-target effects on nontarget organisms (NTOs) in a manner that may be unique to this novel sequence-specific mode of action is crucial. To address this, we propose here a bioinformatics framework for consideration of sequence-specific off-target effects in NTOs. This framework includes careful consideration of NTOs based on potential exposure and susceptibility and recommends standardizing analyses to search for 21-nucleotide stretches of perfect identity and 80% overall identity between the dsRNA and off-target transcripts. We recommend a three-pronged approach to ensure a comprehensive risk assessment: (a) phylogenetic analysis of gene orthologs that defines the taxonomic scope of sequence similarity, (b) broad searches of large databases to identify potential unexpected similarity in distantly related species, and (c) full transcriptome analyses in NTO species of particular concern for a thorough understanding of all potential hazards. Finally, we recommend considering the results of bioinformatic analyses in the context of risk characterization, which means considering likely exposure to the dsRNA-based pesticide and potential susceptibility or barriers to dsRNA uptake. This approach enables a robust ecological risk assessment for dsRNA-based biopesticides and a regulatory path forward for this promising new pest management tool.},
}

*RNA, Double-Stranded/toxicity
Risk Assessment/methods
*Computational Biology/methods
*Biological Control Agents/toxicity
*Pest Control, Biological/methods
Animals
*Pesticides/toxicity

@article {pmid41488433,
year = {2025},
author = {LE, HA and Potter, V and Choube, A and Lakshminarayanan, R and Mishra, V and Intille, S},
title = {A Context-Assisted, Semi-Automated Activity Recall Interface Allowing Uncertainty.},
journal = {Proceedings of the ACM on interactive, mobile, wearable and ubiquitous technologies},
volume = {9},
number = {4},
pages = {},
pmid = {41488433},
issn = {2474-9567},
abstract = {Measuring activities and postures is an important area of research in ubiquitous computing, human-computer interaction, and personal health informatics. One approach that researchers use to collect large amounts of labeled data to develop models for activity recognition and measurement is asking participants to self-report their daily activities. Although participants can typically recall their sequence of daily activities, remembering the precise start and end times of each activity is significantly more challenging. ACAI is a novel, context-assisted ACtivity Annotation Interface that enables participants to efficiently label their activities by accepting or adjusting system-generated activity suggestions while explicitly expressing uncertainty about temporal boundaries. We evaluated ACAI using two complementary studies: a usability study with 11 participants and a two-week, free-living study with 14 participants. We compared our activity annotation system with the current gold-standard methods for activity recall in health sciences research: 24PAR and its computerized version, ACT24. Our system reduced annotation time and perceived effort while significantly improving data validity and fidelity compared to both standard human-supervised and unsupervised activity recall approaches. We discuss the limitations of our design and implications for developing adaptive, human-in-the-loop activity recognition systems used to collect self-report data on activity.},
}

@article {pmid41488255,
year = {2025},
author = {Li, R and Li, J and , and , and , and , and Blaxter, ML},
title = {The genome sequence of the Atlantic Strawberry Cockle, Americardia media (Linnaeus, 1758) (Cardiida: Cardiidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {630},
pmid = {41488255},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Americardia media (Atlantic Strawberry Cockle; Mollusca; Bivalvia; Cardiida; Cardiidae). The assembly contains two haplotypes with total lengths of 1 299.87 megabases and 1 284.99 megabases. Most of haplotype 1 (99.42%) is scaffolded into 19 chromosomal pseudomolecules. Haplotype 2 was assembled to scaffold level. The mitochondrial genome has also been assembled, with a length of 47.2 kilobases.},
}

@article {pmid41484280,
year = {2026},
author = {Lancaster, T and Tut, G and Sylla, P and Bone, D and Bentley, C and Spalkova, E and Jadir, A and Bruton, R and Spencer, K and Mallick, S and Elzaidi, A and Plass, S and Kaur, N and Butler, M and Hulme, S and Dowell, AC and Krutikov, M and Stirrup, O and Azmi, B and Hayward, A and Copas, A and Shallcross, L and Moss, P},
title = {Endemic penetrance of SARS-CoV-2 has impacted marginally on immunity to spike protein of human coronaviruses.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09474-x},
pmid = {41484280},
issn = {2399-3642},
support = {1400035//RCUK | Medical Research Council (MRC)/ ; National Core Study 1644507//RCUK | MRC | Medical Research Foundation/ ; },
abstract = {SARS-CoV-2 has emerged as the 5th endemic coronavirus and immunological cross protection between coronaviruses will influence their infectivity and clinical impact. We determined adaptive immunity against the spike protein of each human coronavirus during the course of the COVID-19 pandemic. A characteristic pattern of HCoV immunodominance, dominated by OC43 and 229E, was apparent prior to SARS-CoV-2 and was largely unaffected by SARS-CoV-2 infection, which itself elicited moderate antibody titre. Vaccination or hybrid immunity elicited supraphysiological levels of coronavirus-specific antibodies, only a proportion of which was cross-reactive with SARS-CoV-2 spike indicating substantial backboosting of HCoV-specific responses. SARS-CoV-2 vaccination focused antibody responses against the S1 domain of SARS-CoV-2 spike whilst T cell responses recognised peptides equivalently across S1 and S2. Coronavirus-specific T cells exhibited strong production of IFN-γ, IL-2 and CXCL8. In summary, the entry of SARS-CoV-2 into its ecological niche has impacted marginally on relative immunity against other human coronaviruses although vaccination provides a modest antibody increment which is unlikely to be maintained. Further, although SARS-CoV-2 vaccination elicits spike-specific adaptive immune responses that are focused against the S1 domain, thereby favouring neutralising antibodies, the natural history of HCoV immunity indicates that adaptive responses may transition towards S2 recognition across the life course.},
}