@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.},
}

@article {pmid41299059,
year = {2025},
author = {Sharma, AK and Jani, AD and Brunnengraeber, E and Choi, J and Fife, R and Gandhok, S and Huie, K and Ilano, AB and Lopez, E and Lopez, M and McMillan, O and Parra, A and Pollock, T and Woodbridge, D and Young, R},
title = {Deep learning classification of INSV-associated weeds in Monterey county using a curated RGB image dataset.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45395},
pmid = {41299059},
issn = {2045-2322},
mesh = {*Deep Learning ; *Plant Weeds/classification/virology ; *Image Processing, Computer-Assisted/methods ; *Convolutional Neural Networks ; Plant Diseases/virology ; Malva ; Sonchus ; California ; Datasets as Topic ; },
abstract = {Weeds, defined by their ecological and economic impact rather than taxonomy, present a major challenge to agriculture by competing with crops for limited resources and serving as vectors for disease. In Monterey County, California, one of the most productive farming regions in the United States, Sonchus oleraceus (annual sowthistle) and Malva parviflora (little mallow) have been linked to over $150 million in crop losses due to their role in spreading Impatiens Necrotic Spot Virus (INSV). As precision agriculture becomes more important in high-value production systems, deep learning and image-based classification offer promising tools for early weed detection and disease prevention. To address the absence of region-specific image datasets, this study presents the first curated, high-resolution image collection of INSV-associated weeds from Monterey County, captured under greenhouse conditions designed to mimic field variability. This dataset fills a documented gap in existing global repositories such as PlantCLEF and DeepWeeds, which lack representation of California's high-value crop systems. This study compares three convolutional neural networks-ResNet-50, ResNet-101, and DenseNet-121-for classifying these visually similar weeds under controlled conditions that approximate real field environments. RGB images were augmented to improve model robustness, and training was conducted across ten independent stratified data splits.Among the tested architectures, ResNet-101 achieved the highest median classification accuracy (91%) and Cohen's Kappa (0.87), while DenseNet-121 demonstrated the strongest F1-score and AUC values exceeding 0.99. These results confirm that dataset augmentation substantially enhanced model generalization. The results demonstrate that deep learning can support accurate and reliable weed identification, paving the way for real-time detection systems and more targeted, sustainable weed control practices in precision agriculture.},
}

*Deep Learning
*Plant Weeds/classification/virology
*Image Processing, Computer-Assisted/methods
*Convolutional Neural Networks
Plant Diseases/virology
Malva
Sonchus
California
Datasets as Topic

@article {pmid41315930,
year = {2025},
author = {Chaussard, A and Bonnet, A and Le Corff, S and Sokol, H},
title = {TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {1},
pmid = {41315930},
issn = {1471-2105},
mesh = {*Metadata ; Humans ; *Gastrointestinal Microbiome ; Machine Learning ; *Microbiota ; *Software ; *Computational Biology/methods ; Algorithms ; },
abstract = {BACKGROUND: The gut microbiome plays a crucial role in human health, making it a cornerstone of modern biomedical research. To study its structure and dynamics, machine learning models are increasingly used to identify key microbial patterns associated with disease and environmental factors, but their performance is often limited by the intrinsic complexity of microbiome data and the small size of available cohorts. In this context, data augmentation has emerged as a promising strategy to overcome these challenges by generating artificial microbiome profiles.

RESULTS: We introduce TaxaPLN, a data augmentation method based on PLN-Tree generative models, which leverages the taxonomy and a data-driven sampler to generate realistic synthetic microbiome compositions. Additionally, we propose a conditional extension based on feature-wise linear modulation, enabling covariate-aware generation. Experiments on diverse curated microbiome datasets show that TaxaPLN preserves ecological properties and generally improves or maintains predictive performances, outperforming state-of-the-art baselines on most tasks. Furthermore, the conditional variant of TaxaPLN establishes a new benchmark for metadata-aware microbiome augmentation.

CONCLUSION: TaxaPLN provides a model-based framework for augmenting microbiome datasets while preserving their ecological and clinical relevance. By integrating taxonomic structure and host metadata, it enhances predictive modeling across diverse real-world settings. To facilitate reproducible and scalable microbiome analysis using our method, TaxaPLN is released as an open-source Python package available on PyPI (plntree), with MIT-licensed source code hosted at https://github.com/AlexandreChaussard/PLNTree-package .},
}

*Metadata
Humans
*Gastrointestinal Microbiome
Machine Learning
*Microbiota
*Software
*Computational Biology/methods
Algorithms

@article {pmid41483326,
year = {2026},
author = {Liu, Z and Liu, W and Wang, S and Wang, X and Zhu, J and Wang, D and Dong, C and Cheng, G and Mei, Y and Qi, X},
title = {Divergent occupational heat stress strategies required for Northern and Southern China under climate change.},
journal = {International journal of biometeorology},
volume = {70},
number = {1},
pages = {6},
pmid = {41483326},
issn = {1432-1254},
support = {2025A04J5097//Guangzhou Basic and Applied Basic Research Foundation/ ; 42301021//National Natural Science Foundation of China/ ; },
mesh = {*Climate Change ; China/epidemiology ; *Heat Stress Disorders/epidemiology/economics/prevention & control ; Humans ; Hot Temperature ; Climate Models ; *Occupational Exposure ; },
abstract = {Observable climate change has led to an increase in compound heat events, thereby amplifying the economic impacts of labor heat stress and necessitating intervention strategies. Current research lacks high-resolution precision in projecting future heat stress and quantifying adaptation strategies, which is particularly critical for China given its spatial disparities in climate, workforce distribution, and economic development. This study integrates high-resolution CMIP6 climate models, a Wet-bulb Globe Temperature (WBGT) algorithm, and localized Exposure-response Functions (ERFs) to project heat-induced labor productivity loss across China under the SSP5-8.5 scenario. It systematically analyzes and quantitatively compares the effectiveness of two adaptation strategies (shading and work schedule adjustments) while estimating direct economic losses in outdoor heavy labor industries. This study precisely identifies the thermal stress hotspots categorized as primary (South China: loss rate > 11%, increment 5-7%), secondary (middle-lower Yangtze River: 7-11% loss, 3-5% increment), and tertiary hotspots (Yangtze River Delta & North China Plain: 6-9% loss, 2-4% increment) based on productivity loss magnitudes. Our findings also reveal that optimal strategies diverge north-south along the 33°N: shading dominates in the south and schedule adjustments in the north due to distinct heat patterns, though future climate trends may reduce the efficacy of time shift adjustments nationwide. Additionally, economic loss estimation reveals surging heat-induced losses in agriculture and construction over two decades (annual growth rates of 11.16% and 20.69%, respectively), with combined strategies potentially reducing direct losses by 65-70% in hotspot provinces. These findings enable province- and industry-specific intervention designs considering regional climate variations and strategy effectiveness.},
}

*Climate Change
China/epidemiology
*Heat Stress Disorders/epidemiology/economics/prevention & control
Humans
Hot Temperature
Climate Models
*Occupational Exposure

@article {pmid41474484,
year = {2025},
author = {Kinkpe, L and Solomon, AI and Niu, Y and Goswami, N and Ikele, CM and Hu, D and Abdessan, R and Zhigang, H and Xia, W},
title = {A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {17},
pmid = {41474484},
issn = {1573-0972},
support = {2023YFD1300300//National Key Research and Development Program of China/ ; (CARS-42-2)//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Livestock/microbiology ; *Gastrointestinal Microbiome ; *Genomics/methods ; *Microbiota ; Computational Biology/methods ; Machine Learning ; Multiomics ; },
abstract = {The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.},
}

Animals
*Livestock/microbiology
*Gastrointestinal Microbiome
*Genomics/methods
*Microbiota
Computational Biology/methods
Machine Learning
Multiomics

@article {pmid41474351,
year = {2026},
author = {Beumer, LT and Hertel, AG and Royauté, R and Tucker, MA and Albrecht, J and Beltran, RS and Cagnacci, F and Davidson, SC and Dejid, N and Kays, R and Kölzsch, A and Lohr, A and Neuschulz, EL and Safi, K and Scharf, AK and Schleuning, M and Wikelski, M and Mueller, T},
title = {MoveTraits-A Database for Integrating Animal Behaviour Into Trait-Based Ecology.},
journal = {Ecology letters},
volume = {29},
number = {1},
pages = {e70297},
doi = {10.1111/ele.70297},
pmid = {41474351},
issn = {1461-0248},
support = {//Hessian Ministry of Science and Research, Arts and Culture, Germany/ ; 80NSSC21K1182//NASA's Ecological Forecasting Program/ ; 101086640//HORIZON EUROPE Research and Innovation Programme/ ; 01LC2320A//German Federal Ministry for Research, Technology and Aeronautics/ ; HE 8857/1-1//Deutsche Forschungsgemeinschaft/ ; NE1863/2-2//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Databases, Factual ; *Birds/physiology ; *Behavior, Animal ; *Ecology/methods ; *Mammals/physiology ; Ecosystem ; Biodiversity ; },
abstract = {Trait-based approaches are key to understanding eco-evolutionary processes but rarely account for animal behaviour despite its central role in ecosystem dynamics. We propose integrating behaviour into trait-based ecology through movement traits-standardised and comparable measures of animal movement derived from biologging data, such as daily displacements or range sizes. Accounting for animal behaviour will advance trait-based research on species interactions, community structure and ecosystem functioning. Importantly, movement traits allow for quantification of behavioural reaction norms, offering insights into species' acclimation and adaptive capacity to environmental change. We outline a vision for a 'living' global movement trait database that enhances trait data curation by (1) continuously growing alongside shared biologging data, (2) calculating traits directly from individual-level data using standardised, consistent methodology and (3) providing information on multi-level (species, individual, within-individual) trait variation. We present a proof-of-concept 'MoveTraits' database with 52 mammal and 97 bird species, demonstrating calculation workflows for 5 traits across multiple timescales. Movement traits have significant potential to improve trait-based global change predictions and contribute to global biodiversity assessments as Essential Biodiversity Variables. By making animal movement data more accessible and interpretable, this database could bridge the gap between movement ecology and biodiversity policy, facilitating evidence-based conservation.},
}

Animals
*Databases, Factual
*Birds/physiology
*Behavior, Animal
*Ecology/methods
*Mammals/physiology
Ecosystem
Biodiversity

@article {pmid41472845,
year = {2025},
author = {Zhu, Z and Zhang, L and Yao, X and Zeng, M and Wang, Y and Luo, H and Zhou, Y and Zhang, T and Xun, J and Bai, D and Yang, H and Xu, S and Zhou, Y and Gao, Y and Xu, J and Han, W and Shen, Z and Zhang, B and Ma, T and Wan, XL and Ma, C and Hui, F and Bai, H and Bai, L and Bai, Q and Bao, Q and Cao, G and Cao, P and Cao, Q and Chen, H and Chen, J and Chen, J and Chen, L and Chen, T and Chen, Y and Cui, H and Dai, S and Dai, XJ and Dai, X and Dang, Y and Deng, L and Deng, Y and Ding, X and Dong, B and Dong, L and Dou, S and Du, H and Fang, Z and Feng, X and Fu, M and Gao, Y and Gong, W and Guo, X and Han, W and Hao, Z and He, ZG and Hu, H and Hu, H and Hu, X and Huang, L and Huang, X and Huang, X and Hui, H and Jia, D and Jiang, A and Jiang, D and Jiang, K and Jiang, D and Jin, Y and Lai, K and Li, C and Li, F and Li, F and Li, J and Li, J and Li, J and Li, K and Li, L and Li, M and Li, P and Li, P and Li, R and Li, S and Li, S and Li, W and Li, W and Li, X and Li, X and Li, X and Liang, Q and Liao, X and Liu, B and Liu, C and Liu, C and Liu, D and Liu, F and Liu, J and Liu, J and Liu, S and Liu, T and Liu, W and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Y and Liu, Z and Liu, Z and Lu, X and Luo, X and Ma, G and Meng, J and Meng, Y and Miao, R and Miao, L and Ni, Y and Niu, D and Niu, T and Pan, H and Qin, G and Qiu, T and Qiu, Y and Qu, H and Qu, L and Ren, N and Sun, Q and Shang, R and She, P and Shen, X and Shi, B and Shu, Y and Song, J and Song, W and Su, Q and Sun, Q and Sun, Y and Sun, Z and Tang, B and Tang, D and Tang, H and Tao, Y and Teng, T and Tu, Y and Wang, C and Wang, H and Wang, Y and Wang, C and Wang, D and Wang, G and Wang, J and Wang, K and Wang, M and Wang, S and Wang, S and Wang, X and Wang, XC and Wang, Y and Wang, J and Wang, Z and Wang, W and Wei, Y and Xu, W and Wu, F and Wu, J and Wu, S and Xiao, J and Xiao, W and Xiao, Y and Xiong, X and Xiong, X and Xu, F and Xu, J and Xu, W and Xu, J and Xu, Y and Yan, J and Yao, L and Yang, J and Yang, L and Yang, X and Yin, N and You, H and You, M and Yu, T and Yu, Y and Yu, R and Yuan, S and Yue, C and Zeng, X and Zha, A and Zhai, L and Zhang, C and Zhang, D and Zhang, H and Zhang, H and Zhang, H and Zhang, J and Zhang, J and Zhang, L and Zhang, Q and Zhang, X and Zhang, X and Zhang, X and Zhang, Y and Zhang, Y and Zhang, Z and Zhao, J and Zhao, J and Zhao, K and Zhao, M and Zhao, Y and Zhao, Y and Zhong, J and Zhong, L and Zhong, X and Zhou, D and Zhou, W and Zhou, W and Zhou, Y and Zhou, Z and Zhu, S and Liu, SJ and Feng, S and Jin, S and Xiao, C and Wang, Z and Luo, P and Chen, T and Chen, G and Liu, YX},
title = {iMeta Conference 2025: Creating high-impact international journals.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70086},
pmid = {41472845},
issn = {2770-596X},
abstract = {The iMeta Conference 2025, part of the iMeta Conference series, themed "Creating High-Impact International Journals," held at the Huangjiahu Campus of Hubei University of Chinese Medicine from August 23rd to 25th, 2025, and focused on frontier topics such as microbiology, medicine, traditional Chinese medicine, botany, and research career development. The event aimed to support the development of researchers and strengthen the impact of academic journals. Through invited reports, thematic seminars, and poster presentations, the conference highlighted hot topics including multi-omics technologies, microbe-host interactions, AI-assisted research, live biotherapeutic products, and the modernization of traditional Chinese medicine. The event demonstrated the innovative momentum of interdisciplinary integration and technological convergence, providing an international platform for academic exchange and laying a foundation for building an innovative scientific research ecosystem and enhancing the global influence of Chinese academic journals.},
}

@article {pmid41472087,
year = {2025},
author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D},
title = {Correction: Schalli et al. Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources. Microorganisms 2022, 10, 2499.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472087},
issn = {2076-2607},
abstract = {In the original publication [...].},
}

@article {pmid41468864,
year = {2025},
author = {Cho, YJ and Kim, KH and Suh, DW and Baek, IS and Phee, JH and Yu, JY and Kim, KM and Park, YR},
title = {Shadow-Induced Forgetting in a Game-Based Paradigm on Nonclinical Adults and Its Effects on Consciousness, Emotional Valence, and Temporal Dynamics: Crossover Study.},
journal = {JMIR serious games},
volume = {13},
number = {},
pages = {e76946},
doi = {10.2196/76946},
pmid = {41468864},
issn = {2291-9279},
abstract = {BACKGROUND: Memory suppression transiently disrupts hippocampal activity, leading to suppression-induced forgetting, especially for negative stimuli. However, traditional paradigms such as Think/No-Think rely on explicit control and lack ecological validity. This study introduces a game-based task that implicitly elicits suppression through reversed motor mappings, providing a naturalistic approach to studying memory inhibition.

OBJECTIVE: This study aims to examine how shadow-induced forgetting (ShIF) varies across short-term and long-term intervals (0 hours, 24 hours, and 72 hours), under conscious versus unconscious exposure, and between positive and negative emotional stimuli.

METHODS: This single-center, within-subjects experimental study involved 56 university students (mean age 23.37, SD 1.84 years) and was conducted between December 1, 2023, and March 1, 2024. Participants learned 36 cue-target image pairs varying in emotional valence (positive and negative). They underwent a game-based paradigm where habitual motor responses were disrupted through reversed key mappings to induce an amnesic shadow. During gameplay, selected cues were presented either consciously or unconsciously, while others served as controls. Memory performance was assessed using Metric for Evaluation of Translation with Explicit Ordering scores (semantic similarity) immediately after intervention (0 hour) and again at 24 hours and 72 hours. Electroencephalography was recorded in a subset of 40 participants to examine neural correlates of memory suppression.

RESULTS: ShIF effects were short-term, conscious-dependent, and selective for negative memories. A significant interaction between exposure condition and time (F₃.₆₂,₁₉₉.₃₃=2.7, P=.04, η²p=0.05, 95% CI 0.00-1.00) indicated that the effect varied across time points. Specifically, a significant ShIF effect emerged immediately after the intervention (0 hour) in the conscious condition (t₅₅=-2.86, P=.02, d=0.38) but was absent in the unconscious condition and dissipated by 72 hours. Robust main effects of time (F₂,₁₀₉.₉₉=102.91, P<.001, η²p=0.65, 95% CI 0.57-1.00) and emotional valence (F₁,₅₅=42.43, P<.001, η²p=0.44, 95% CI 0.27-1.00) showed that overall recall declined over time and was consistently lower for negative images. Electroencephalography analyses revealed enhanced right frontal beta (FC6, F4, and F8: P<.001) and posterior gamma (O1: P<.001, O2: P<.001, and P8: P=.002) activity during suppression of negative cues, reflecting neural inhibition processes underlying ShIF.

CONCLUSIONS: ShIF occurs primarily for consciously processed negative memories and diminishes over several days, highlighting the temporal and emotional boundaries of intentional forgetting. This study introduces a game-based approach that extends traditional suppression paradigms and offers an ecologically valid framework for investigating memory control. Importantly, we demonstrate that suppression can be induced through a game-based paradigm. By examining emotional valence, exposure condition, and temporal dynamics, we extend previous work focused only on transient effects and clarify the potential for practical implementation in digital therapeutic applications such as posttraumatic stress disorder treatment.},
}

@article {pmid41452932,
year = {2025},
author = {Giral Martínez, J and Barbier, M and De Monte, S},
title = {Interplay of structured and random interactions in complex ecosystems dynamics.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013786},
doi = {10.1371/journal.pcbi.1013786},
pmid = {41452932},
issn = {1553-7358},
mesh = {*Ecosystem ; *Models, Biological ; Computational Biology ; Population Dynamics ; Computer Simulation ; Animals ; },
abstract = {Minimal models for complex ecosystems often assume random interactions, whose statistics suffice to predict dynamical and macroecological patterns. However, ecological networks commonly possess a variety of properties, such as hierarchies or functional groups, that structure species interactions. Here, we ask how conclusions from random interaction models are altered by the presence of such community-level network structures. We consider a Lotka-Volterra model where pairwise species interactions combine structure and randomness, and study macroscopic community-level observables, abundance distributions and dynamical regimes. Randomness and structure combine in a surprisingly yet deceptively straightforward way: contributions from each component to community patterns are largely independent. Yet, their interplay has non-trivial consequences, notably out of equilibrium. We conclude that whether interaction structure matters depends on the pattern: when breaking species equivalence, static patterns of species presence and abundance predicted from random interaction models are less robust than the qualitative nature of dynamical regimes.},
}

*Ecosystem
*Models, Biological
Computational Biology
Population Dynamics
Computer Simulation
Animals

@article {pmid41429884,
year = {2025},
author = {Song, W and Hu, Q and Liu, S and Hou, Y},
title = {Decadal spatiotemporal dynamics of surface water bodies in Zhengzhou, China: remote sensing monitoring and analysis of driving factors.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45089},
pmid = {41429884},
issn = {2045-2322},
abstract = {Water is essential for life, human activities, and ecological balance. Understanding the spatiotemporal dynamics of urban water bodies is critical for sustainable water management, especially in fast-growing cities like Zhengzhou. This study investigates the evolution of water bodies in Zhengzhou from 2014 to 2023, using multi-seasonal Landsat 8 imagery and GIS analysis. Three water extraction methods-thresholding, random forest (RF), and a hybrid RF model incorporating spectral indices (NDWI, MNDWI, EWI) and GLCM-based texture features-were evaluated. The hybrid RF approach demonstrated the highest classification accuracy and was applied to generate seasonal water body maps for the target years. The results show a general increase in surface water area, with seasonal peaks in July–September, and spatial expansion mainly in the northern and northeastern regions. These changes are driven by both natural (e.g., precipitation) and anthropogenic (e.g., urban development, artificial lake construction) factors. Compared to previous studies, this research offers three key innovations: (1) a decade-long, seasonal-scale analysis of water dynamics; (2) a robust multi-feature classification framework for complex urban settings; and (3) an integrated interpretation of natural and human influences. The findings provide valuable references for water resource planning and urban ecological restoration, and the methods used may be transferable to similar inland cities under monsoon climates.},
}

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {Ecosystem ; *Metagenome ; Microbiota ; Pacific Ocean ; *RNA, Transfer/genetics ; *Seawater/microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

Ecosystem
*Metagenome
Microbiota
Pacific Ocean
*RNA, Transfer/genetics
*Seawater/microbiology
*Transcriptome
Datasets as Topic

@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; *Estuaries ; Eukaryota/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Viruses/genetics ; Datasets as Topic ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}

Archaea/genetics
Bacteria/genetics
Biodiversity
Ecosystem
*Estuaries
Eukaryota/genetics
*Geologic Sediments/microbiology
Metagenomics
Viruses/genetics
Datasets as Topic

@article {pmid41467398,
year = {2025},
author = {Sugimoto, N and Matsugaki, R and Cooray, U and Kuhara, S and Onoue, T and Saeki, S and Muramatsu, K and Fushimi, K and Matsuda, S and Murakami, M and Ikeda, T},
title = {Safety of Early Rehabilitation for Acute Heart Failure Using Japanese Medical Claims.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e045953},
doi = {10.1161/JAHA.125.045953},
pmid = {41467398},
issn = {2047-9980},
abstract = {BACKGROUND: The safety of initiating early physical rehabilitation therapy and its optimal load in patients with acute decompensated heart failure (ADHF) remain unclear. This study evaluated the safe timing and load of early rehabilitation therapy for patients with ADHF.

METHODS: In this cohort study using nationwide medical claims data from Japan, we included patients aged ≥18 years who were admitted for ADHF and received in-hospital rehabilitation therapy for at least 2 days within the first 4 days of admission between 2016 and 2020. Nine hypothetical treatment regimens within the first 7 days of admission, varying in timing, duration, and load were used as exposures. The outcome was the cumulative incidence of adverse events (eg, death) within 30 days after admission. A per-protocol analysis was conducted using a target trial emulation framework with a sequential doubly robust estimator.

RESULTS: Altogether, 10 179 patients with ADHF were enrolled, with 752 developing adverse events (incidence 7.39%). The lowest incidence rate (4.13%) was observed in the regimen where therapy was initiated on the first day of admission with 20 minutes of therapy, continuing for up to 7 days (95% CI, 3.30-4.95). Conversely, the highest incidence rate was observed in the regimen where therapy was initiated on the third day of admission with 40 minutes of therapy, continuing for up to 7 days (8.67% [95% CI, 8.22-9.13]).

CONCLUSIONS: Very early, low-load rehabilitation therapy for patients with ADHF may reduce the risk of adverse events. These findings suggest important implications in the implementation of early rehabilitation.},
}

@article {pmid41464893,
year = {2025},
author = {Yan, R and Chen, Z and Zhou, S and Niu, G and Li, Y and Liu, Z and Wang, J and Wu, X and Luo, Q and Zhou, Y and Jin, Y and Liu, K and Yuan, W and Xu, J and Xu, F},
title = {ForestFoodKG: A Structured Dataset and Knowledge Graph for Forest Food Taxonomy and Nutrition.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
doi = {10.3390/foods14244186},
pmid = {41464893},
issn = {2304-8158},
abstract = {Forest foods play a vital role in enhancing dietary diversity, human health, and the sustainable use of forest ecosystems. However, structured and machine-readable resources that systematically describe their taxonomic and nutritional attributes remain scarce. To fill this gap, we introduce ForestFoodKG, a comprehensive resource that integrates taxonomic hierarchy and nutritional composition of 1191 forest food items. The resource consists of two components-(i) the ForestFoodKG dataset, containing standardized taxonomic and nutritional records across seven biological levels, and (ii) the ForestFoodKG Knowledge Graph (ForestFoodKG-KG), which semantically links forest food entities using named entity recognition and relation extraction. The constructed graph comprises 4492 entities and 14,130 semantic relations, providing a structured foundation for intelligent querying, nutrition analytics, and ecological informatics. All data were manually verified and made publicly available in CSV format on GitHub. ForestFoodKG serves as the first structured knowledge base for forest foods, promoting data-driven research in nutrition science, sustainable forestry, and knowledge-based decision-making.},
}

@article {pmid41464285,
year = {2025},
author = {Alkattan, A and Norful, AA and Pan, CX and August, P and Crupi, RS and Schwartz, JE and Miele, A and Brondolo, E},
title = {Monitoring Redeployment-Associated Burnout in Healthcare Workers: A Real-Time Approach Using Ecological Momentary Assessment.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {24},
pages = {},
doi = {10.3390/healthcare13243217},
pmid = {41464285},
issn = {2227-9032},
support = {1K08MH130652-01/NH/NIH HHS/United States ; },
abstract = {Background/Objectives: Ecological momentary assessment (EMA) is a methodology that offers a real-time approach to monitoring clinician well-being, but its utility during high-intensity operational periods remains underexplored. This study examines the feasibility and performance of an EMA-based system for tracking clinical responsibilities and burnout among healthcare workers during the first year of the COVID-19 pandemic. Methods: Utilizing an intensive longitudinal design, 398 healthcare workers, including physicians, physician assistants, nurses, and trainees, completed brief EMA surveys every five days from April 2020 to March 2021. Burnout was assessed with a validated single-item measure and analyzed in relation to redeployment status and hospital caseloads. Results: The EMA approach successfully captured meaningful temporal fluctuations in burnout. Redeployment was associated with higher burnout levels (b = 0.125; p = 0.01), and rising caseloads amplified this effect (interaction b = 0.169; p = 0.001). Nurses showed the strongest caseload-related increases in burnout (b = 0.359; p < 0.001). These patterns persisted even after individuals returned to their usual roles. Conclusions: This study demonstrates that EMA is a scalable and sensitive approach for continuous burnout surveillance, capable of detecting role-specific and context-dependent stress responses in real time. EMA-based monitoring can support early identification of at-risk groups, guide staffing and redeployment decisions, and inform timely organizational interventions during crises and other periods of operational strain.},
}

@article {pmid41461568,
year = {2025},
author = {Liu, Y and Luo, Z and Xiao, Y and Li, Y and Liu, M and Shi, Y and Li, Z and Lei, W and Li, C and Jin, LN and Yan, W},
title = {Microplastics in Motion: How Earthworm Guts Become Microbial Gateways through Plastic Surface Dynamics.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15257},
pmid = {41461568},
issn = {1520-5851},
abstract = {Microplastics (MPs) pollution in terrestrial ecosystems poses significant ecological risks, particularly as carriers of microbial communities and potential pathogens. However, the mechanisms by which MPs interact with microbes during transit through soil animal digestive systems remain poorly understood. This study investigated the interactions between poly(ethylene terephthalate) (PET) and polystyrene (PS) MPs and gut-derived microbes using a biomimetic earthworm gut model. PET and PS MPs exhibited distinct microbial colonization patterns, driven by their physicochemical properties. PET MPs, with rougher surfaces, preferentially adsorbed cocci such as Paraclostridium, fostering high-density but low-activity bacterial populations. Conversely, PS MPs, with smoother surfaces, enriched bacilli such as Raoultella, supporting low-density but high-activity bacterial communities. PET MPs facilitated rapid bacterial proliferation but lacked long-term stability, whereas PS MPs created persistent microenvironments that increased the ecological risk of pathogen retention and spread. The oxidative degradation of MPs during gut transit enhanced bacterial adhesion by forming reactive surface functionalities. MPs significantly altered microbial diversity and served as selective vectors for microbial dissemination into soil ecosystems, disrupting the microbial dynamics. These findings underscore the dual role of MPs as microbial scaffolds and ecological disruptors, providing critical insights into their ecological impacts and guiding strategies to mitigate MP contamination and pathogenic risks.},
}

@article {pmid41318763,
year = {2025},
author = {Turek, S and Skarzyńska-Łyżwa, A and Aparna, A and Pląder, W and Riewe, D and Junker, A and Altmann, T and Pawełkowicz, M},
title = {Multi-omics integration of transcriptome, miRNA, and metabolome uncovers molecular mechanisms of male flower development in cucumber line B10 (Cucumis sativus L.).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45734},
pmid = {41318763},
issn = {2045-2322},
support = {UMO-2020/37/B/NZ9/00586//Narodowe Centrum Nauki/ ; CUC_GC-MS//European Plant Phenotyping Network - EPPN/ ; },
mesh = {*Cucumis sativus/genetics/growth & development/metabolism ; *Flowers/genetics/growth & development/metabolism ; *MicroRNAs/genetics/metabolism ; Gene Expression Regulation, Plant ; *Transcriptome ; *Metabolome ; Gene Expression Profiling ; Metabolomics/methods ; Multiomics ; },
abstract = {Male flower development in cucumber (Cucumis sativus L.) is a highly coordinated and genetically regulated process, yet the full complexity of its molecular underpinnings remains incompletely understood. In this study, we present a comprehensive, multi-omics analysis of male flower development in the cucumber line B10, integrating transcriptomic (RNA-seq), small RNA (miRNA) profiling, and metabolomic data across key tissues, including leaves, shoot apex, and floral buds at distinct developmental stages. Our analyses reveal dynamic gene expression changes and novel regulatory miRNAs, several of which have not previously been linked to male bud formation in cucumber. Functional enrichment analyses using GO and KEGG highlight critical pathways, including starch and sucrose metabolism, carbohydrate utilization, sporopollenin biosynthesis, and lignin catabolism. An integrative analysis combining miRNA-target interactions, transcriptomic shifts, and differential metabolite accumulation revealed coherent regulatory cascades linking transcription factors, carbohydrate metabolism, and cell wall dynamics. This study provides novel insights into the intricate genetic and metabolic networks shaping male flower morphogenesis and provides a valuable resource for advancing cucumber reproductive biology and crop improvement strategies.},
}

*Cucumis sativus/genetics/growth & development/metabolism
*Flowers/genetics/growth & development/metabolism
*MicroRNAs/genetics/metabolism
Gene Expression Regulation, Plant
*Transcriptome
*Metabolome
Gene Expression Profiling
Metabolomics/methods
Multiomics

@article {pmid41257544,
year = {2025},
author = {Agany, DD and Callegari, EA and Paez, MD and Pietri, JE},
title = {Multi-omics of cockroaches infected with Salmonella Typhimurium identifies molecular signatures of vector colonization.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1118},
pmid = {41257544},
issn = {1471-2164},
support = {P20GM103443/NH/NIH HHS/United States ; R01AI171014/NH/NIH HHS/United States ; P20GM103443/NH/NIH HHS/United States ; R01AI171014/NH/NIH HHS/United States ; },
mesh = {Animals ; *Salmonella typhimurium/physiology ; *Cockroaches/microbiology/genetics/metabolism ; *Proteomics/methods ; Host-Pathogen Interactions ; Transcriptome ; Gene Expression Profiling ; *Insect Vectors/microbiology/genetics ; Multiomics ; },
abstract = {BACKGROUND: German cockroaches (Blattella germanica) are prevalent indoor pests that have long been associated with the spread of enteric human pathogens. Recent work investigating the relationship between these insects and Salmonella enterica serovar Typhimurium (S. Typhimurium), a model pathogen of global concern, demonstrated that S. Typhimurium colonizes the cockroach gut. S. Typhimurium has a broad host range, but mechanistic molecular insight into how ecologically relevant invertebrate hosts interact with this pathogen is lacking. Here, we applied a multi-omic (transcriptomic and proteomic) approach to infected cockroaches to examine the molecular variables that govern cockroach-borne S. Typhimurium transmission.

RESULTS: Our results reveal enriched monocarboxylic acid transport and metabolism, increased long-chain fatty acid transport, increased triglyceride metabolism, and an increased response to reactive oxygen species and free radicals as host signatures of a metabolic shift in the cockroach gut during infection. Surprisingly, downregulation of the immune deficiency (IMD) pathway transcription factor relish, and upregulation of xenobiotic detoxification (glutathione-s-transferase) and known allergens (Blag5 & Blag8, myosin, tropomyosin) were also evident in infected guts.

CONCLUSIONS: To our knowledge, this study is both the first omics study of enteric human pathogen infection in a cockroach vector and the first omics study of S. Typhimurium in an ecologically relevant insect host, representing a seminal contribution to the field of vector-borne infectious disease. This work provides novel fundamental knowledge regarding the response of insect hosts to S. Typhimurium infection and the evolution of vector-pathogen relationships with the potential to inform mitigation of the public health impacts of cockroaches.},
}

Animals
*Salmonella typhimurium/physiology
*Cockroaches/microbiology/genetics/metabolism
*Proteomics/methods
Host-Pathogen Interactions
Transcriptome
Gene Expression Profiling
*Insect Vectors/microbiology/genetics
Multiomics

@article {pmid41459590,
year = {2025},
author = {Holmqvist, S and Shou, H and Halberstadter, K and Kaplan, M and Chaturvedi, R and Rhodes, E and Giovannetti, T},
title = {Bidirectional associations of daily mood and subjective cognition in older adults using Ecological Momentary Assessment.},
journal = {Aging & mental health},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/13607863.2025.2606875},
pmid = {41459590},
issn = {1364-6915},
abstract = {OBJECTIVES: Depressive symptoms and subjective cognition are linked in older adults, but traditional measures have numerous limitations that may be addressed by ecological momentary assessment (EMA). This study examined whether baseline depressive and cognitive measures correspond to daily EMA ratings and evaluated concurrent and lagged relations between mood and subjective cognition.

METHOD: Fifty-five community-dwelling older adults (31% Black/African American; 44 cognitively healthy, 11 mild cognitive impairment) completed a four-week daily EMA survey assessing mood and subjective cognition. Baseline measures included a global cognitive composite and self-reported depressive symptoms, functional independence, and cognitive decline. Cumulative link mixed models examined associations between baseline and EMA measures and concurrent and lagged EMA relations.

RESULTS: EMA mood correlated with baseline depressive symptoms, while EMA subjective cognition was most strongly associated with functional independence rather than objective cognition or self-reported cognitive decline. EMA mood and cognition were reciprocally associated concurrently. In lagged models, worse EMA subjective cognition predicted worse next-day mood, whereas the reverse association was not statistically significant. Lagged effects were attenuated after accounting for temporal trends and prior-day EMA values.

CONCLUSION: EMA provides low-burden insights into mood and subjective cognition, supporting its utility for naturalistic assessment in older adults.},
}

@article {pmid41458448,
year = {2025},
author = {Lin, S and Zhang, M and Feng, L and Lu, M and Liu, X},
title = {Spatio-temporal evolution and influencing factors of cultural heritage embedded cultural tourism efficiency.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1690535},
pmid = {41458448},
issn = {2296-2565},
mesh = {Humans ; China ; *Tourism ; *Spatio-Temporal Analysis ; },
abstract = {Enhancing the efficiency of cultural tourism serves as a critical catalyst for the synergistic development of culture and the economy. However, existing research has primarily focused on the content of the cultural tourism industry and its coupling coordination relationships, while comparatively little attention has been given to incorporating key resources-such as cultural heritage-into analytical frameworks access efficiency and underlying impact mechanisms. This study introduces an innovative perspective that embeds cultural heritage within the evaluation process. To address the issue of intertemporal and regional comparability, the Super SBM-DEA model is employed to measure the efficiency of cultural heritage embedded cultural tourism (CHECTE) across 30 Chinese provinces from 2012 to 2022 and identifies its driving factors through Tobit regression. The findings demonstrate that average efficiency exhibits a "declining-rising-declining" pattern over the observed period. Specifically, efficiency decreased to 0.5829 in 2015, reached a peak of 0.8511 in 2019, and then experienced a subsequently decline. During periods of decline, efficient areas contract toward the central and western regions, whereas during periods of improvements, these areas expand into the southwest and southeast. This spatial dynamic reveals a notable departure from traditional regional economic gradients. The central region attained a higher average efficiency of 0.7499 compared to the eastern region of 0.5746, suggesting that the central region derives greater benefits from cultural heritage resources than its eastern counterpart. Tobit regression results reveal that transportation conditions, informatization level, policy environment, higher education, and technological innovation are the key driving factors, with significant regional differences. The eastern region is primarily driven by technological innovation and consumption demand, the central region by the policy environment and informatization, and the western region by transportation conditions and higher education. This study offers theoretical and practical guidance for resource allocation and region-specific cultural tourism policies.},
}

Humans
China
*Tourism
*Spatio-Temporal Analysis

@article {pmid41458310,
year = {2025},
author = {Feiner, N and Uller, T and Abalos, J and Slimani, T and S'Khifa, A and Meier, J and , and , and , and , },
title = {The genome sequence of the Andalusian wall lizard, Podarcis vaucheri (Boulenger, 1905).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {265},
pmid = {41458310},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Podarcis vaucheri (Andalusian wall lizard; Chordata; Lepidosauria; Squamata; Lacertidae). The assembly contains two haplotypes with total lengths of 1,614.91 megabases and 1,510.74 megabases. Most of haplotype 1 (98.26%) is scaffolded into 20 chromosomal pseudomolecules, including the W and Z sex chromosomes. Most of haplotype 2 (98.63%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 17.24 kilobases.},
}

@article {pmid41455740,
year = {2025},
author = {Deb, N and Rahman, T and Moniruzzaman, M and Bin Obadi, AS and Jizat, NM and Al-Bawri, SS and Rahman, AAM},
title = {Integrating feature selection and explainable CNN for identification and classification of pests and beneficial insects.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-32520-x},
pmid = {41455740},
issn = {2045-2322},
abstract = {Reliable identification of agricultural pests and beneficial insects is crucial for sustainable crop protection and ecological balance, yet most vision-based models remain black boxes and require high-dimensional features. This paper proposes an explainable hybrid insect-classification framework that combines convolutional neural network (CNN) feature extraction with a dual-XAI feature selection strategy. SHapley Additive exPlanations (SHAP) and Permutation Feature Importance (PFI) are applied in parallel to rank handcrafted and CNN-derived features, and their intersection yields a compact, biologically meaningful subset for final classification. The selected features are evaluated using lightweight classifiers and a hybrid ensemble, enabling accurate inference under field variability. Experiments on a curated, balanced dataset of four classes (Colorado potato beetle, green peach aphid, seven-spot ladybird, and healthy leaves) collected under diverse lighting and background conditions achieve 96.7% overall accuracy, with precision, recall, and F1-scores all above 96%. Importantly, performance remains stable when reducing dimensionality, retaining ≥90% accuracy using only the top 11 hybrid-selected features. These results demonstrate that integrating SHAP and PFI improves both robustness and interpretability, supporting practical deployment for automated pest monitoring and precision agriculture.},
}

@article {pmid41290686,
year = {2025},
author = {Niedostatek, M and Baptista, A and Yamamoto, J and Kurths, J and Sanchez Garcia, R and MacArthur, BD and Bianconi, G},
title = {Mining higher-order triadic interactions.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11613},
pmid = {41290686},
issn = {2041-1723},
mesh = {Humans ; Algorithms ; Leukemia, Myeloid, Acute/genetics/metabolism ; *Data Mining/methods ; Neural Networks, Computer ; },
abstract = {Complex systems often involve higher-order interactions that go beyond pairwise networks. Triadic interactions, where one node regulates the interaction between two others, are a fundamental form of higher-order dynamics found in many biological systems, from neuron-glia communication to gene regulation and ecosystems. However, triadic interactions have so far been mostly neglected. In this article, we propose the Triadic Perceptron Model (TPM) which shows that triadic interactions can modulate the mutual information between the dynamical states of two connected nodes. Leveraging this result, we formulate the Triadic Interaction Mining (TRIM) algorithm to extract triadic interactions from node metadata, and we apply this framework to gene expression data, finding new candidates for triadic interactions relevant for Acute Myeloid Leukemia. Our findings highlight crucial aspects of triadic interactions that are often ignored, offering a framework that can deepen our understanding of complex systems across biology, ecology, and climate science.},
}

Humans
Algorithms
Leukemia, Myeloid, Acute/genetics/metabolism
*Data Mining/methods
Neural Networks, Computer

@article {pmid41450553,
year = {2025},
author = {Hao, W and Shan, YF and Kimura, T and Ukawa, S and Ohira, H and Okabayashi, S and Wakai, K and Ando, M and Tamakoshi, A},
title = {Effect modification by dietary patterns in the relationship between slow gait and incident depressive symptoms: a 6-year cohort study of older Japanese adults (NISSIN Project).},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1698581},
pmid = {41450553},
issn = {2296-861X},
abstract = {INTRODUCTION: Slower gait speed is a well-established predictor of late-life depressive symptoms. Previous research suggests that diet can influence biological processes implicated in both gait decline and depression and may therefore serve as an effect modifier in their association. This study aimed to examine whether adherence to healthy dietary patterns modifies the relationship between gait speed and incident depressive symptoms in older adults.

METHODS: In this longitudinal observational cohort study, we analyzed data from 1,887 depression-free, community-dwelling adults aged 64-65 years, obtained from the New Integrated Suburban Seniority Investigation (NISSIN) Project in Japan. Gait speed was self-rated at baseline as fast, normal, or slow. Dietary intake was assessed using a validated food frequency questionnaire (FFQ), and principal component analysis was performed to identify three dietary patterns: vegetables, Fat and Meat, and Bread and Egg. Incident depressive symptoms were defined as having a 15-item Geriatric Depression Scale (GDS-15) score of ≥6 after a 6-year follow-up. Modified Poisson regression was used to estimate relative risks (RRs), and interactions were assessed on multiplicative and additive scales.

RESULTS: After 6 years, 12.5% of the participants developed depressive symptoms. Slow gait speed was significantly associated with a higher risk of depression (RR: 2.7; 95% CI: 1.6-4.6), while no dietary pattern was independently associated with depressive symptoms. This risk tended to be lower among slow walkers with higher adherence to a vegetable or Bread and Egg dietary pattern, although the interactions were not statistically significant. A significant negative interaction was found between slow gait and low adherence to a Fat and Meat diet on both additive (RERI = -2.5; 95% CI: -4.1 to -0.8) and multiplicative scales (Ratio of RRs: 0.3; 95% CI: 0.2-0.3).

DISCUSSION: Dietary patterns may influence the link between slow gait and depression in older adults. Notably, reduced adherence to Fat and Meat diets was associated with a lower overall risk. These findings support dietary improvement as a scalable mental health strategy for physically vulnerable older adults.},
}

@article {pmid41446515,
year = {2025},
author = {Mehrotra, S and Duggal, C and Rustagi, N and Ransing, RS and Indu, PS and Chakraborty, S and Mene, T and Sharma, P and Prasad, D and Prinja, S and Verma, P and Dhamija, RK and Kataria, K and Munivenkatappa, M and Suthar, N and Anilkumar, TV and Dahiya, N and Grover, A},
title = {Multistate study on suicide risk reduction and improving mental well-being among school and college students in India - an implementation research study protocol.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1708246},
pmid = {41446515},
issn = {2296-2565},
mesh = {Humans ; India ; *Suicide Prevention ; *Students/psychology/statistics & numerical data ; Universities ; Adolescent ; Young Adult ; *Mental Health ; *Risk Reduction Behavior ; Male ; Female ; Suicide/psychology ; Schools ; Research Design ; },
abstract = {UNLABELLED: Suicide remains a crucial public health concern in India, especially among students and young adults. The growing academic pressure, social stigma, and lack of accessible mental health services contribute to the growing crisis and suicide rates in India. The study aims to develop an implementation model for educational institutions for reducing risk of suicide behavior (perceived stress and depressive symptoms) and enhance help-seeking behavior. This multi-sectoral implementation model is grounded in the WHO's recommendation for youth suicide prevention and UMMEED guidelines. The study will adopt a concurrent mixed methods design, incorporating both quantitative and qualitative aspects that would be captured simultaneously. A formative research phase will be initially conducted before taking on the main study and it will be guided by the Updated Consolidated Framework for Implementation Research (CFIR). Additionally, the evaluation of the implementation process will be structured using the RE-AIM framework. The study participants will be school and pre-university students, and college students The expected outcome will be achieving reduction of suicide risk behaviors among school and college students in selected districts. The key barriers and facilitators identified through this implementation research will inform recommendations for the potential nation-wide scale up of strategies aimed suicide prevention strategies at educational institutes.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, CTRI/2024/08/072027.},
}

Humans
India
*Suicide Prevention
*Students/psychology/statistics & numerical data
Universities
Adolescent
Young Adult
*Mental Health
*Risk Reduction Behavior
Male
Female
Suicide/psychology
Schools
Research Design

@article {pmid41435586,
year = {2025},
author = {Zeng, T and Du, H and Wu, R},
title = {The chemical structures, and biological activities of marine terpenoids: a review and perspective from cheminformatics.},
journal = {Chinese journal of natural medicines},
volume = {23},
number = {12},
pages = {100006},
doi = {10.1016/j.cjnm.2025.100006},
pmid = {41435586},
issn = {1875-5364},
mesh = {*Terpenes/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; *Biological Products/chemistry/pharmacology ; *Cheminformatics ; Humans ; Animals ; Molecular Structure ; Anti-Inflammatory Agents/chemistry/pharmacology ; Antineoplastic Agents/chemistry/pharmacology ; },
abstract = {Marine terpenoids are a structurally diverse class of natural products produced by marine organisms, characterized by unique molecular architectures and notable biological activities. They play essential roles in ecological interactions and chemical defense, while also exhibiting promising therapeutic properties, including anti-inflammatory and anti-tumor effects. In this review, we compile 13 132 reported marine terpenoids, of which 2066 have documented biological activities, and provide a concise summary of their organismal origins, molecular scaffolds, and associated activities. Cheminformatics approaches are further applied to compare the chemical space of marine versus terrestrial terpenoids, highlighting their structural distinctiveness. Finally, we discuss promising directions for the discovery, utilization, and synthesis of marine terpenoids, with the goal of promoting comprehensive and sustainable exploration of these valuable marine resources.},
}

*Terpenes/chemistry/pharmacology
*Aquatic Organisms/chemistry
*Biological Products/chemistry/pharmacology
*Cheminformatics
Humans
Animals
Molecular Structure
Anti-Inflammatory Agents/chemistry/pharmacology
Antineoplastic Agents/chemistry/pharmacology

@article {pmid41307499,
year = {2025},
author = {Campbell, R and Mevers, E},
title = {Structural Characterization and Multiomics Analysis Reveal Extensive Diversity and Global Distribution of Kurstakin Lipopeptides.},
journal = {Journal of natural products},
volume = {88},
number = {12},
pages = {2960-2967},
doi = {10.1021/acs.jnatprod.5c01212},
pmid = {41307499},
issn = {1520-6025},
mesh = {*Lipopeptides/chemistry ; Molecular Structure ; *Bacillus cereus/chemistry ; Multiomics ; },
abstract = {Bacillus species, particularly those investigated as biocontrol agents, are known to produce a cocktail of bioactive lipopeptides that act synergistically to shape the ecological function of these beneficial microbes. However, while certain families of lipopeptides are well-characterized, others remain elusive. Herein, we describe the characterization of the kurstakins, a family of lipopeptides associated with promising biocontrol properties but that lack adequate characterization. Metabolomic analyses of a semipurified Bacillus cereus EM195W extract fraction revealed the presence of approximately 50 cyclic- and linear-peptide analogs. Deeper analyses revealed that the chemical diversity stems from the diverse lipid tails, including linear, iso-, and anteiso-lipid tails ranging from C8-C18, along with several hydroxylated lipid tails. Isolation and complete structural analysis of two new analogs represented the first kurstakin analogs characterized by NMR and provided the first experimental analyses for deducing their absolute configuration. Finally, analysis of publicly available genomic and MS data provided insights into the true chemical diversity and distribution of the kurstakins. These results expand our understanding of this family of compounds, opening the door for determining their ecological functions and the role they play in the broader activity of biocontrol agents.},
}

*Lipopeptides/chemistry
Molecular Structure
*Bacillus cereus/chemistry
Multiomics

@article {pmid41289675,
year = {2026},
author = {Zou, D and Fancello, G and Montanari, A and Zhou, S and Chaix, B},
title = {Momentary associations between time-varying social contacts and depressive symptomatology in older adults: A GPS-based mobility survey study.},
journal = {Social science & medicine (1982)},
volume = {389},
number = {},
pages = {118834},
doi = {10.1016/j.socscimed.2025.118834},
pmid = {41289675},
issn = {1873-5347},
mesh = {Humans ; Male ; Female ; Aged ; *Depression/psychology/epidemiology ; France/epidemiology ; Ecological Momentary Assessment ; Bayes Theorem ; Geographic Information Systems/statistics & numerical data ; Surveys and Questionnaires ; Aged, 80 and over ; Time Factors ; Middle Aged ; *Interpersonal Relations ; },
abstract = {Studies often investigate the long-term impact of social contacts on mental health in older adults, neglecting momentary effects. This research, grounded in the consideration of daily activity, explores how time-varying social contacts associate with momentary depressive symptoms among 216 older adults in the Île-de-France region. Employing a geographically-explicit ecological momentary assessment approach (GEMA), we collected participants' depressive symptoms, mobility locations, and social contacts data via smartphone surveys, GPS receivers, and mobility survey over 7 days. Bayesian mixed models with random effects at individual and daily levels, considering time autocorrelation, were employed. Participants engaging with social contacts exhibited lower depression not only immediately but also in the following hours. Interestingly, a longer duration of time spent with social contacts did not lead to a sharper decrease in depression levels. Notably, larger decreases were observed when the number of social contacts increased from one to two, especially with friends or family members.},
}

Humans
Male
Female
Aged
*Depression/psychology/epidemiology
France/epidemiology
Ecological Momentary Assessment
Bayes Theorem
Geographic Information Systems/statistics & numerical data
Surveys and Questionnaires
Aged, 80 and over
Time Factors
Middle Aged
*Interpersonal Relations

@article {pmid41443831,
year = {2025},
author = {Okuda, N and Nakamura, K and Watanabe, M and Kamide, K and Yoshita, K and Torii, S and Miura, K and Higashiyama, A and Tanno, K and Yonekura, Y and Nagahata, T and Kuribayashi, T and Okayama, A},
title = {Factors Affecting Body Weight/Waist Circumference Changes after Specific Health Guidance for Obese People with CVD Risk Factors in Japan.},
journal = {Journal of atherosclerosis and thrombosis},
volume = {},
number = {},
pages = {},
doi = {10.5551/jat.65943},
pmid = {41443831},
issn = {1880-3873},
abstract = {AIM: Specific Health Checkups (SHCs) and Specific Health Guidance (SHG) were launched in 2008, but the factors related to their effectiveness have not been clarified. We examined the mean reduction in body weight (BW) and waist circumference (WC) of participants eligible for active support under SHG. Body size was considered, as well as the number of support points given during SHG, which indicates the amount of support they received.

METHODS: A dataset of participants (aged 40-64) who were eligible for SHG and had SHC results collected between 2011 and 2012 was analyzed (n = 76,565). The mean changes in BW and WC between 2011 and 2012 were compared among participants based on their participation status (did not participate, dropped out, finished) and the number of support points for those who finished. Participants were also stratified by sex and BMI (kg/m[2]): normal weight, overweight, and obese.

RESULTS: The mean BW change (95% CI) for those who did not participate and finished SHG was -0.45 kg (-0.47, -0.43) and -1.32 kg (-1.39, -1.25) in men, and -0.66 kg (-0.72, -0.60) and -1.68 kg (-1.87, -1.49) in women, respectively. Higher support points and larger body sizes correlated with greater reductions in BW in men (P＜0.001), but the associations were not significant in women. The reduction in WC was greater in women with normal weight than in obese women.

CONCLUSION: Sex differences were observed in the association between BW/WC reduction and body size or the amount of support given during SHG.},
}

@article {pmid41438403,
year = {2025},
author = {Khaleghi, P and Cakir, D and Hamidoğlu, A and Gul, OM and Kadry, S},
title = {Interpretable deep learning for depression detection in neurological patients using EEG signals.},
journal = {MethodsX},
volume = {15},
number = {},
pages = {103736},
pmid = {41438403},
issn = {2215-0161},
abstract = {Depression affects over 280 million people worldwide, with neurological patients particularly prone to medication-induced episodes. Conventional diagnostic approaches rely on subjective evaluations, limiting reproducibility and consistency in clinical settings. This study proposes an interpretable deep learning framework for objective depression detection using EEG signals. We hypothesize that combining EEG-based features with explainable artificial intelligence can provide both high accuracy and transparency in diagnosis. The model was trained on EEG data from 232 neurological patients, achieving 98 % classification accuracy. Interpretability was enhanced through SHAP (SHapley Additive exPlanations) analysis, which identified clinically meaningful EEG biomarkers such as the delta/alpha ratio and theta band power. This paper highlights the following contributions: Integration of EEG features with a lightweight deep learning model for depression detection High diagnostic accuracy achieved while maintaining interpretability for clinicians An objective tool that is compatible with existing EEG infrastructure, supporting clinical adoption These results show that our framework bridges predictive performance with interpretability, offering a transparent and scalable EEG-based diagnostic tool. We conclude that this approach can complement clinical decision-making, reducing dependence on subjective evaluation and enabling more consistent, data-driven mental health care.},
}

@article {pmid41436485,
year = {2025},
author = {Sardeshpande, M and Bangira, T and Azong Cho, M and Matongera, TN and Mabhaudhi, T},
title = {Exploring the social-ecological potential for indigenous agroforestry in peri-urban areas: a participatory mapping approach.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44344},
pmid = {41436485},
issn = {2045-2322},
support = {205200/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Forestry/methods ; Humans ; South Africa ; Geographic Information Systems ; *Agriculture/methods ; Conservation of Natural Resources ; Socioeconomic Factors ; },
abstract = {Peri-urban agroforestry can provide affordable, fresh, and nutritious food and a departure from conventional forms of cropping. Indigenous foods are well-adapted to local conditions, and may hold cultural and economic value for peri-urban residents. Social, ecological, and economic variables influence the feasibility of indigenous agroforestry in peri-urban areas. This study uses participatory mapping and geographic information systems (GIS) to assess these variables and to map suitable spaces and species for peri-urban indigenous agroforestry at three peri-urban sites in Durban, South Africa. We find that: land tenure, livelihood opportunities, and indigenous food perceptions factor into socioeconomic preferences; topography and soil quality influence ecological feasibility; access to water and roads influences perceived economic viability. Although GIS techniques can identify land suitability, participatory mapping adds local fine-scale context to enhance decision-making. Based on the social-ecological conditions at the three sites, we suggest specific configurations of locally adapted foods and farm designs for peri-urban agroforestry. Our study demonstrates how agroforestry is more feasible in places where basic living conditions are fulfilled, and how co-design can improve recognition of local needs, accessibility to services, and balancing urban green equity.},
}

*Forestry/methods
Humans
South Africa
Geographic Information Systems
*Agriculture/methods
Conservation of Natural Resources
Socioeconomic Factors

@article {pmid41432923,
year = {2025},
author = {Pu, SY and Lu, JS and Tao, XL and Li, ZF and Wang, YN and Zhang, HM and Lu, X},
title = {The Odonata of China: a data-driven, open-access resource for biodiversity research and conservation.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf077},
pmid = {41432923},
issn = {1758-0463},
support = {202401BC070017//Yunnan Fundamental Research Projects/ ; //Yunnan Revitalization Talent Support Program Yunling Scholar Project (Xuemei Lu)/ ; XDA0460405//Chinese Academy of Sciences/ ; 202505AT350003//Chinese Academy of Sciences/ ; 202405AS350022//Chinese Academy of Sciences/ ; 202305AD160021//Yunnan Technology Innovation Talent Program/ ; },
mesh = {China ; *Biodiversity ; Animals ; *Conservation of Natural Resources ; *Odonata/genetics/classification ; *Databases, Factual ; Phylogeny ; },
abstract = {Odonata (dragonflies and damselflies) are among the most ancient winged insects, with over 900 species recorded in China, representing the highest global diversity. However, the lack of a centralized database integrating morphological, ecological, and multiomics data has hindered large-scale research and conservation efforts. We present Odonata of China (http://dragonflies.kiz.ac.cn), a comprehensive database compiling taxonomic, biogeographic, phenotypic, and multiomics data for 820 species across 3 suborders, 22 families, and 172 genera. The database features advanced search modules (direct, phylogenetic, and map-based), genomic and transcriptomic data for 20 representative families, and high-resolution images. The platform is constructed based on mainstream open-source technologies, ensuring scalability and reproducibility. Odonata of China provides a critical resource for evolutionary biology, conservation, and ecological studies. By integrating heterogeneous data types and leveraging modern technologies, this database bridges a significant gap in invertebrate biodiversity informatics and supports global initiatives to monitor insect declines.},
}

China
*Biodiversity
Animals
*Conservation of Natural Resources
*Odonata/genetics/classification
*Databases, Factual
Phylogeny

@article {pmid41432418,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0037425},
doi = {10.1128/jb.00374-25},
pmid = {41432418},
issn = {1098-5530},
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase-variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes, including colony morphology, cell elongation, and cell chaining in C. difficile. Here, we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state, leading to chaining and a rough colony morphology. This phenomenon is most pronounced with E. faecalis, as other enterococcal species and select Gram-negative enteric bacteria do not show a similar effect. These results suggest that the composition of the polymicrobial environment in the gut is critical to influencing C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.IMPORTANCEClostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.},
}

@article {pmid41432067,
year = {2025},
author = {Banse, SA and Sedore, CA and Coleman-Hulbert, A and Johnson, E and Onken, B and Hall, D and Segerdell, E and Jackson, EG and Song, Y and Osman, HC and Xue, J and Basttistoni, E and Guo, S and Foulger, A and Achanta, M and Sheikh, M and Fitzgibbon, T and Willis, JH and Woodruff, GC and Driscoll, M and Lithgow, G and Phillips, PC},
title = {Computer prediction and genetic analysis identifies retinoic acid modulation as a driver of conserved longevity pathways in genetically diverse Caenorhabditis nematodes.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.104375},
pmid = {41432067},
issn = {2050-084X},
support = {AG045844/NH/NIH HHS/United States ; AG045864/NH/NIH HHS/United States ; AG045829/NH/NIH HHS/United States ; AG056052/NH/NIH HHS/United States ; },
mesh = {Animals ; *Longevity/drug effects/genetics ; *Tretinoin/metabolism/pharmacology ; *Caenorhabditis elegans/genetics/drug effects/physiology ; Signal Transduction/drug effects ; Caenorhabditis elegans Proteins/metabolism/genetics ; Computational Biology ; },
abstract = {Discovery of new compounds that ameliorate the negative health impacts of aging promises to be of tremendous benefit across a number of age-based comorbidities. One method to prioritize a testable subset of the nearly infinite universe of potential compounds is to use computational prediction of their likely anti-aging capacity. Here, we present a survey of longevity effects for 16 compounds suggested by a previously published computational prediction set, capitalizing upon the comprehensive, multi-species approach utilized by the Caenorhabditis Intervention Testing Program. While 11 compounds (aldosterone, arecoline, bortezomib, dasatinib, decitabine, dexamethasone, erlotinib, everolimus, gefitinib, temsirolimus, and thalidomide) either had no effect on median lifespan or were toxic, 5 compounds (all-trans retinoic acid, berberine, fisetin, propranolol, and ritonavir) extended lifespan in Caenorhabditis elegans. These computer predictions yield a remarkable positive hit rate of 30%. Deeper genetic characterization of the longevity effects of one of the most efficacious compounds, the endogenous signaling ligand all-trans retinoic acid (atRA, designated tretinoin in medical products), demonstrated a requirement for the regulatory kinases AKT-1 and AKT-2. While the canonical Akt-target FOXO/DAF-16 was largely dispensable, other conserved Akt-targets (Nrf2/SKN-1 and HSF1/HSF-1), as well as the conserved catalytic subunit of AMPK AAK-2, were all necessary for longevity extension by atRA. Our results highlight the potential of combining computational prediction of longevity interventions with the power of nematode functional genetics and underscore that the manipulation of a conserved metabolic regulatory circuit by co-opting endogenous signaling molecules is a powerful approach for discovering aging interventions.},
}

Animals
*Longevity/drug effects/genetics
*Tretinoin/metabolism/pharmacology
*Caenorhabditis elegans/genetics/drug effects/physiology
Signal Transduction/drug effects
Caenorhabditis elegans Proteins/metabolism/genetics
Computational Biology

@article {pmid41427890,
year = {2025},
author = {Martin, SLF and La Torre, R and Danneels, B and Tooming-Klunderud, A and Skage, M and Kollias, S and Tørresen, OK and Anbaran, MF and Stur, E and Jakobsen, KS and Martin, MD and Ekrem, T},
title = {Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf160},
pmid = {41427890},
issn = {2047-217X},
abstract = {BACKGROUND: Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date.

FINDINGS: We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (D. hyperborea, D. lindrothi, D. serratosioi and D. tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation.

CONCLUSIONS: Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.},
}

@article {pmid41348937,
year = {2025},
author = {Xu, X and Cai, Z and Jia, W and Cao, Y and Hao, Y and Zhou, X and Liang, A and Lin, Z and Zhuang, S and Zhang, Z and Han, L and Zhao, J and White, JC and Ma, C and Xing, B},
title = {Multiomics Insights into Nanoscale Boron Nitride Mediated Antioxidant Defense and Metabolic Reprogramming in Cucumber in Response to Fusarium Infection.},
journal = {ACS nano},
volume = {19},
number = {50},
pages = {42349-42364},
doi = {10.1021/acsnano.5c14128},
pmid = {41348937},
issn = {1936-086X},
mesh = {*Fusarium/drug effects ; *Antioxidants/metabolism/pharmacology/chemistry ; *Plant Diseases/microbiology ; *Boron Compounds/pharmacology/chemistry ; *Cucumis sativus/metabolism/microbiology/drug effects ; *Nanoparticles/chemistry ; Oxidative Stress/drug effects ; Metabolic Reprogramming ; Multiomics ; },
abstract = {Fusarium poses a significant threat to the global crop productivity and food security. This study evaluated the mechanisms of nanoscale boron nitride (nano-BN, 0-500 mg/kg) against Fusarium oxysporum in cucumber. Fusarium infection severely impaired plant growth with biomass declining by 60%. However, 50 mg/kg nano-BN treatment significantly increased shoot biomass by 64.9% compared to disease controls, restoring photosynthetic parameters to near-healthy levels. Nano-BN inhibited Fusarium proliferation by disrupting hyphal and spore structures and reduced mycotoxin production (beauvericin and enniatin) by over 63%. Metabolomic analysis demonstrates that nano-BN mitigated oxidative stress by enhancing glutathione metabolism, with significant increases in glutathione and ascorbic acid content by 166.67% and 478.78%, respectively. Importantly, the protein-protein interaction network shows that nano-BN counteracted Fusarium-induced suppression of ribosomal proteins and endoplasmic reticulum stress-related proteins, promoting protein synthesis and folding. The coexpression network identified sucrose and geshoidin as key metabolites linked to ribosomal and mitochondrial proteins, bridging metabolic resilience with enhanced disease resistance. Multiomics analysis suggests that nano-BN alleviated the Fusarium stress by regulating the phenylpropanoid biosynthesis and restoring the expression levels of key enzymes in carbohydrate metabolism. Overall, nano-BN effectively mitigates Fusarium stress by enhancing plant growth and modulating metabolic processes, offering a promising strategy for plant protection.},
}

*Fusarium/drug effects
*Antioxidants/metabolism/pharmacology/chemistry
*Plant Diseases/microbiology
*Boron Compounds/pharmacology/chemistry
*Cucumis sativus/metabolism/microbiology/drug effects
*Nanoparticles/chemistry
Oxidative Stress/drug effects
Metabolic Reprogramming
Multiomics

@article {pmid41319542,
year = {2026},
author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W},
title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147314},
doi = {10.1016/j.foodchem.2025.147314},
pmid = {41319542},
issn = {1873-7072},
mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation & purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; },
abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.},
}

*Flavoring Agents/metabolism/chemistry
*Bacteria/genetics/metabolism/isolation & purification/classification
Gas Chromatography-Mass Spectrometry
Taste
*Alcoholic Beverages/analysis/microbiology
Volatile Organic Compounds/chemistry/metabolism
*Wine/analysis/microbiology
Microbial Consortia
Metabolomics
Multiomics

@article {pmid41271865,
year = {2025},
author = {Pottier, P and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Yang, Y and Varon, S and Longo, AV and Burke, S and Lin, HY and Valdebenito, JO and Amano, T and Drobniak, SM and Nakagawa, S and Claunch, N},
title = {AmphiTherm: a comprehensive database of amphibian thermal tolerance and preference.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1987},
pmid = {41271865},
issn = {2052-4463},
support = {Scientia PhD Scholarship//University of New South Wales (UNSW Australia)/ ; Scientia PhD scholarship//University of New South Wales (UNSW Australia)/ ; DP230101248//Department of Education and Training | Australian Research Council (ARC)/ ; FT220100276//Department of Education and Training | Australian Research Council (ARC)/ ; FT180100354//Department of Education and Training | Australian Research Council (ARC)/ ; DE180100202//Department of Education and Training | Australian Research Council (ARC)/ ; UPD2024-0239//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; DFG-FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; IOS-2011278//National Science Foundation (NSF)/ ; 2109663//National Science Foundation (NSF)/ ; 3220722//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; },
mesh = {Animals ; *Amphibians/physiology ; *Thermotolerance ; Biodiversity ; Databases, Factual ; },
abstract = {Thermal traits are crucial to our understanding of the ecology and physiology of ectothermic animals. While rising global temperatures have increasingly pushed research towards the study of upper thermal limits, lower thermal limits and thermal preferences are essential for defining the thermal niche of ectotherms. Through a systematic review of the literature in seven languages, we expanded an existing database of amphibian heat tolerance by adding 1,009 estimates of cold tolerance and 816 estimates of thermal preference across 375 species. AmphiTherm is a comprehensive and reproducible database that contains 4,899 thermal trait estimates from a diverse sample of 659 species (~7.5% of all described amphibians) spanning 38 families. Despite its broad geographic coverage, we report evident gaps across amphibian biodiversity hotspots in Africa, most regions of Asia, central South America, and Western Australia. By providing a more holistic understanding of amphibian thermal tolerance and preferences, AmphiTherm is a valuable resource for advancing research in evolutionary biology, ecophysiology, and biogeography of amphibians, offering insights that are increasingly needed in changing climates.},
}

Animals
*Amphibians/physiology
*Thermotolerance
Biodiversity
Databases, Factual

@article {pmid41258717,
year = {2025},
author = {Cheng, R and Lv, T and Ji, P and Ma, B and Wang, M and Matsumoto, H},
title = {Multi-omics analyses reveal the virulence differentiation underlying natural variation in Burkholderia gladioli.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0168525},
doi = {10.1128/aem.01685-25},
pmid = {41258717},
issn = {1098-5336},
support = {2024SZRZDC130001//Natural Science Foundation of Hangzhou/ ; LD25C140002//Zhejiang Provincial Natural Science Foundation of China/ ; U21A20219//National Natural Science Foundation of China/ ; W2533054//National Natural Science Foundation of China/ ; 2024M762853//China Postdoctoral Science Foundation/ ; },
mesh = {*Burkholderia gladioli/genetics/pathogenicity ; *Oryza/microbiology ; Virulence/genetics ; *Plant Diseases/microbiology ; *Genetic Variation ; Bacterial Proteins/genetics/metabolism ; Genome, Bacterial ; Transcriptome ; Multiomics ; },
abstract = {UNLABELLED: Burkholderia gladioli is a critical pathogen causing bacterial panicle blight in rice, severely threatening global rice yield and grain quality. Here, B. gladioli strains were isolated and identified from two rice fields exhibiting markedly different severities of bacterial panicle blight. Although the two strains belong to the same species, they displayed significant differences in phenotype and pathogenicity. Comparative genomic and transcriptomic analyses revealed that natural variation between the strains not only arose from 79 single-nucleotide polymorphisms (SNPs), 12 insertions/deletions (INDELs), and 3 structural variations (SVs) across 27 mutated genes, which may affect protein function and stability, but also coincided with the significant downregulation of genes in multiple virulence-associated pathways, such as two-component systems, bacterial chemotaxis, quorum sensing, and flagellar assembly at the transcriptional level. The combined effects of genetic variation and transcriptional regulation ultimately contributed to the observed differences in pathogenicity. This study uncovers the potential mechanisms by which natural variation in B. gladioli influences pathogenicity, providing a theoretical basis and potential molecular targets for the precise control of rice bacterial panicle blight.

IMPORTANCE: This study demonstrates that natural variation in Burkholderia gladioli, a major pathogen responsible for bacterial panicle blight in rice, has a significant impact on its pathogenicity and further explores the underlying mechanisms. These findings expand our understanding of how phytopathogens' virulence differentiates conditions of natural variation, and provide potential molecular targets for the development of novel bactericides. The identification of low-virulence strains and their associated gene variations in this study offers both theoretical and practical foundations for ecological disease management and biocontrol of rice bacterial diseases, highlighting their importance for promoting precision agriculture and sustainable development.},
}

*Burkholderia gladioli/genetics/pathogenicity
*Oryza/microbiology
Virulence/genetics
*Plant Diseases/microbiology
*Genetic Variation
Bacterial Proteins/genetics/metabolism
Genome, Bacterial
Transcriptome
Multiomics

@article {pmid41427113,
year = {2025},
author = {Garai, S and Vo, S and Blank, L and Xu, F and Chen, J and Duong-Tran, D and Zhao, Y and Brown, BC and Shen, L},
title = {H-VIP: quantifying regional topological contributions of the brain network to cognition.},
journal = {Frontiers in radiology},
volume = {5},
number = {},
pages = {1686780},
pmid = {41427113},
issn = {2673-8740},
abstract = {INTRODUCTION: Understanding the role of various brain regions of interest (ROIs) in various cognitive functions or tasks, across healthy or neurodegenerative conditions and multiple degrees of separation, remains a key challenge in neuroscience. Conventional network measures can only capture localized or quasi-localized features of brain ROIs. Topological data analysis (TDA), particularly persistent homology, provides a threshold-free, mathematically rigorous framework for identifying topologically salient features in complex networks. In this paper, we introduce a new metric, the Homological Vertex Importance Profile (H-VIP), designed to assess the relevance of vertices that participate in persistent topological structures (e.g., connected components, cycles or cavities) in brain networks. The H-VIP quantifies the topological features of the network at the ROI (node) level by compressing its higher-order connectivity profile using homological constructs.

METHODS: Leveraging homological constructs of brain connectomes, we extend two of our previously defined network-level measures-average persistence and persistence entropy-to an ROI-level measure, i.e., the H-VIP. We then applied the H-VIP to two independent datasets: structural connectomes from the Human Connectome Project and functional connectomes from the Alzheimer's Disease Neuroimaging Initiative. Persistent homology was computed for each network, and H-VIP scores were derived to evaluate vertex-level contributions. Finally, H-VIP scores were used for the prediction of multiple cognitive measures.

RESULTS: In both anatomical and functional brain networks, H-VIP values demonstrate predictive power for various cognitive measures. Notably, the connectivity of the frontal lobe exhibited stronger correlations with cognitive performance than the whole-brain network.

DISCUSSION: H-VIP offers a robust and interpretable means to locate, quantify, and visualize region-specific contributions to network's topological, higher-order landscape. Its ability to detect potentially impaired connectivity at the individual level suggests possible applications in personalized medicine for neurological diseases and disorders. Beyond brain connectomics, the H-VIP can be used for other types of complex networks where topological features are of importance, such as financial, social, or ecological networks.},
}

@article {pmid41425965,
year = {2025},
author = {Lin, Y and Chen, S and Che, J and Sun, M and Wang, Y},
title = {Multi-omics approaches for image classification in disease diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616189},
pmid = {41425965},
issn = {2235-2988},
mesh = {Humans ; *Genomics/methods ; *Computational Biology/methods ; *Proteomics/methods ; *Metabolomics/methods ; Multiomics ; },
abstract = {INTRODUCTION: The integration of multi-omics data for disease diagnosis holds transformative potential in the field of computational biology, especially when applied to the intricate and dynamic interactions between microbial communities and their human hosts.

METHODS: This integrative approach enables to capture diverse biological signals across genomic, transcriptomic, proteomic, and metabolomic layers, providing a more comprehensive understanding of disease mechanisms. In alignment with emerging priorities in disease microbiology, our study addresses a critical and timely need for interpretable, scalable, and biologically robust computational models that can extract clinically meaningful diagnostic insights from inherently high-dimensional, heterogeneous, and often incomplete biological datasets.

RESULTS AND DISCUSSION: Traditional image classification approaches in disease contexts-such as those relying solely on histopathological features or genomic imaging-tend to overlook the broader ecological and systemic dimensions that are essential for decoding the mechanisms of microbial pathogenesis. These single-modal methods often suffer from significant limitations, including reduced scalability to diverse clinical settings, poor generalizability across patient populations, and an inability to handle partially observed or biologically variable data. Such constraints diminish their effectiveness in precision diagnostics, disease subtyping, and therapeutic decision-making. By contrast, our approach emphasizes multi-modal integration and model interpretability, aiming to overcome these limitations and advance the development of next-generation diagnostic tools that are both clinically actionable and biologically grounded.},
}

Humans
*Genomics/methods
*Computational Biology/methods
*Proteomics/methods
*Metabolomics/methods
Multiomics

@article {pmid41425596,
year = {2025},
author = {Yu, R and Hasan, A and Ibrahim, M and Alonazi, WB and Bin, L},
title = {An integrated immunoinformatic approach to design a novel multiepitope chimeric vaccine against Mycoplasma phocimorsus as a causal agent of bloodstream infections.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1719398},
pmid = {41425596},
issn = {1664-3224},
mesh = {*Bacterial Vaccines/immunology/genetics ; *Mycoplasma Infections/immunology/prevention & control/microbiology ; Humans ; *Mycoplasma/immunology ; Computational Biology/methods ; Epitopes, B-Lymphocyte/immunology ; Animals ; Epitopes/immunology ; Proteomics/methods ; Vaccine Development ; *Sepsis/immunology/prevention & control/microbiology ; },
abstract = {INTRODUCTION: Mycoplasma phocimorsus is increasingly recognized as an emerging human pathogen, despite its primary association with marine mammals. It has recently been identified as a causative agent of bloodstream infections and sepsis, a major cause of mortality among hospitalized patients. To date, no approved vaccine is available against M. phocimorsus, underscoring the urgent need for preventive strategies.

METHODS: The current study was aimed at employing immunoinformatic approaches to design a vaccine based on multiple epitopes derived from the six core proteomic datasets of representative M. phocimorsus strains.

RESULTS: By subtractive genomics, we retrieved 3,576 nonredundant proteins from M. phocimorsus proteomes following only one putative immunoglobulin-blocking virulence outer membrane protein conserved in six strains. The epitopes derived from the putative immunoglobulin-blocking virulence protein exhibited promising features such as strong binding affinity, lack of allergenicity, nontoxic properties, high antigenicity scores, and excellent solubility. Moreover, these epitopes include nine linear B cell epitopes, eight MHC class I epitopes, and five MHC class II epitopes. In addition, adjuvants and linker molecules were successfully merged into a chimeric vaccine with significant immunogenicity and stimulation of both adaptive and innate immune responses. The promising potential of the selected vaccine candidates was further validated through their favorable physico-chemical characteristics, strong interaction with TLR-4, and stable performance in molecular dynamics simulations.

DISCUSSION: These results suggest that the putative immunoglobulin-blocking outer membrane virulence protein could effectively participate in activating the primary innate immune response, thereby serving as a strong foundation for subsequent adaptive immune activation. The proposed vaccine provides substantial basis for developing effective preventive and therapeutic measures against the zoonotic M. phocimorsus, whose association with sepsis, soft tissue, and respiratory infections, particularly in immunocompromised individuals emphasizes the crucial need for vaccine development.},
}

*Bacterial Vaccines/immunology/genetics
*Mycoplasma Infections/immunology/prevention & control/microbiology
Humans
*Mycoplasma/immunology
Computational Biology/methods
Epitopes, B-Lymphocyte/immunology
Animals
Epitopes/immunology
Proteomics/methods
Vaccine Development
*Sepsis/immunology/prevention & control/microbiology