@article {pmid42419187,
year = {2026},
author = {Abbod, M},
title = {Computational framework integrating subtractive proteomics and structural bioinformatics to nominate candidate fungicide targets in Puccinia graminis f. sp. tritici.},
journal = {Computational biology and chemistry},
volume = {124},
number = {Pt 2},
pages = {109233},
doi = {10.1016/j.compbiolchem.2026.109233},
pmid = {42419187},
issn = {1476-928X},
mesh = {*Proteomics ; *Fungicides, Industrial/chemistry/pharmacology ; *Puccinia/drug effects/chemistry/metabolism ; *Computational Biology ; Molecular Docking Simulation ; *Fungal Proteins/metabolism/chemistry/antagonists & inhibitors ; Triticum/microbiology ; },
abstract = {Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, continues to threaten global wheat production through recurring outbreaks and the erosion of host resistance and chemical control efficacy. This study aimed to identify candidate protein targets for fungicide development in P. graminis f. sp. tritici. An integrated subtractive proteomics pipeline was then applied, combining essentiality screening, pathway analysis, structural modeling, and exploratory molecular docking. A stringent filtering strategy excluding proteins homologous to Triticum aestivum, Homo sapiens, and beneficial microbes (Bacillus subtilis, Pseudomonas fluorescens, and Trichoderma harzianum) was applied, thereby maximizing selectivity while minimizing potential off-target ecological effects. From 36,348 proteins, four putative targets were identified: two β-glucan synthesis-associated KRE6 homologs, a cell wall α-1,3-glucan synthase (AGS1), and a Major Facilitator Superfamily (MFS) transporter. Guided by intrinsic disorder analysis, AlphaFold2 was used to generate high-quality 3D structural models of the prioritized targets. Network-based functional analysis linked these proteins to core cellular processes, while underscoring that their essentiality in P. graminis f. sp. tritici remains experimentally unconfirmed. Molecular docking with the antifungal agent poacic acid and the nucleotide sugar UDP-glucose suggested potential binding interactions within the predicted cavities. These exploratory simulations present preliminary evidence for plausible small-molecule binding pockets in the selected candidate targets. Collectively, this work provides a multi-layered computational framework for nominating and structurally characterizing candidate targets in wheat stem rust and generates testable hypotheses for future experimental work.},
}

*Proteomics
*Fungicides, Industrial/chemistry/pharmacology
*Puccinia/drug effects/chemistry/metabolism
*Computational Biology
Molecular Docking Simulation
*Fungal Proteins/metabolism/chemistry/antagonists & inhibitors
Triticum/microbiology

@article {pmid42485614,
year = {2026},
author = {Zhang, J and Xu, W and Xing, J and Sun, Y and Huang, S and Su, X},
title = {CAM-Net: a context-aware network for identifying reliable microbial relations via optimal consortium.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {4},
pages = {},
pmid = {42485614},
issn = {1477-4054},
support = {2025Z154//Innovation Yongjiang 2035 Key R&D Program/ ; 25-3-1-11-zyyd-jch//Qingdao Natural Science Foundation/ ; 32572519//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Algorithms ; *Computational Biology/methods ; *Microbial Interactions ; },
abstract = {Microbes exist within complex community contexts, particularly for key functional species whose stable colonization critically depends on specific ecological partners. However, conventional microbial correlation analyses predominantly rely on isolated pairwise metrics (e.g. Spearman, SparCC, and FlashWeave), which ignore community-level dependencies. This limitation leads to spurious associations in large-scale datasets and obscures the true structure of microbial interactions. Here, we introduce CAM-Net, a context-aware framework that identifies a target microbe's optimal consortium, a fully connected network subset that accurately predicts its abundance. By constructing networks via multi-hop information propagation, CAM-Net effectively filters false positives from indirect associations and captures complex, context-dependent patterns that are inaccessible to traditional pairwise approaches. We evaluated CAM-Net on over 25 000 human gut microbiome samples using Akkermansia muciniphila and Lactobacillus acidophilus as representatives of indigenous and transient colonizers. CAM-Net identified a coherent and reproducible consortium for A. muciniphila, but only weak association structures for L. acidophilus, consistent with their ecological behaviors. In contrast, pairwise methods produced spurious associations for both species. Notably, despite substantial geographic heterogeneity, Alistipes shahii consistently emerged as a conserved core member of the A. muciniphila consortium, demonstrating the advantage of context-aware modeling. The source code is available at https://github.com/qdu-bioinfo/CAM-Net.},
}

Humans
*Microbiota
Algorithms
*Computational Biology/methods
*Microbial Interactions

@article {pmid42489682,
year = {2026},
author = {Jain, B and Bandodkar, AJ},
title = {Biodegradable and bioresorbable rechargeable batteries: chemistries, AI-driven material discovery, and emerging applications.},
journal = {Materials horizons},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6mh01006g},
pmid = {42489682},
issn = {2051-6355},
abstract = {Biodegradable and bioresorbable rechargeable batteries are emerging as key enabling technologies for transforming the manner in which electronic systems are powered when device retrieval, recycling, or long-term persistence is a challenge or undesirable. This review integrates recent advances in materials engineering and artificial intelligence for creating "green-by-design" secondary batteries that operate safely in the environment and on/within living organisms for a desired timeline before naturally disintegrating into non-toxic materials. The discussion first surveys sustainable chemistries and architectures that collectively enable rechargeable operation and degradation of spent batteries into benign ions and small molecules. Subsequent sections examine how established lithium-ion battery informatics can be repurposed for biodegradable alternatives. Specifically, these sections explore how workflows for property prediction, multi-objective optimization, and literature mining can integrate explicit constraints regarding battery lifetime and environmental toxicity. The review concludes by outlining grand challenges and research priorities required to transition biodegradable secondary batteries from laboratory exemplars into practical power sources intrinsically aligned with their biological and ecological contexts.},
}

@article {pmid42490563,
year = {2026},
author = {Mir, ZR and Pebsworth, P and Hardman, J and Ala'amri, S and Alahmari, A and Almalki, K and Boug, A},
title = {Effects of urban association on the movement ecology of hamadryas baboons (Papio hamadryas) in Saudi Arabia.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0354133},
pmid = {42490563},
issn = {1932-6203},
mesh = {Animals ; Saudi Arabia ; *Papio hamadryas/physiology ; Male ; Ecosystem ; Geographic Information Systems ; Humans ; Movement ; },
abstract = {Human-wildlife conflict involving primates is an emerging conservation concern in rapidly urbanizing regions. The hamadryas baboon (Papio hamadryas), the only native non-human primate of the Arabian Peninsula, increasingly exploits anthropogenic food sources, intensifying human-baboon conflict across southwestern Saudi Arabia. To examine how human-modified environments influence baboon spatial ecology; we fitted GPS collars to ten adult males representing groups that are regarded as living in urban, natural and semi-natural environments across five regions. Over nine months, we collected 13,962 location fixes and analyzed them using empirical variograms, home range analysis, and minimum daily path length estimates. Variogram analyses indicated that baboons living in a natural environment exhibited the greatest space-use extent, semi-natural individuals showed intermediate and more variable space-use dynamics, whereas baboons living in urban areas displayed restricted movement. Hamadryas baboons living in natural environments exhibited the largest home ranges with a median of 8.79 km2 (range: 6.19-13.86 km2) and minimum daily path lengths with median 3.33 km (range 0.02-20.6 km), whereas baboons living in urban areas maintained the smallest ranges with a median of 1.31 km2 (range: 1.24-1.79 km2) and the minimum daily path lengths with a median of 2.16 km (range: 0.01-4.85 km). The proportion of daytime spent in urban areas increased along the gradient, 7.2% (natural), 40.6% (semi-natural), and 55.0% (urban). These findings support the Resource Dispersion Hypothesis, suggesting that food predictability shapes baboon space use more than resource scarcity. The study strengthens ongoing conflict-mitigation efforts by providing insights into baboon movement patterns and supporting the ecological differentiation of natural, semi-natural, and urban baboon groups, thereby informing category-specific management interventions.},
}

Animals
Saudi Arabia
*Papio hamadryas/physiology
Male
Ecosystem
Geographic Information Systems
Humans
Movement

@article {pmid42491029,
year = {2026},
author = {DeSalle, AJ and Agbajelola, VI and Ericsson, AC and Shyu, CR and Palaniappan, K and Shacham, E and Raghavan, RK},
title = {Seasonal variation in the bacterial microbiome of questing nymphal ticks in Missouri, United States.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1863755},
pmid = {42491029},
issn = {1664-302X},
abstract = {BACKGROUND: Seasonal environmental variation may influence the composition of tick-associated bacterial communities. This study assessed seasonal differences in the microbiome of questing nymphal ticks collected from Missouri, United States.

METHODS: Questing ticks were collected during early and late seasonal periods at a livestock-associated site in central Missouri. To minimize confounding by developmental stage, microbiome analyses were restricted to nymphal ticks. Bacterial communities were characterized using 16S rRNA gene sequencing. Alpha diversity (richness, Shannon, and Simpson indices), beta diversity (Jaccard and Bray-Curtis dissimilarities), and differential abundance analyses were performed. Community differences were evaluated using permutational multivariate analysis of variance (PERMANOVA).

RESULTS: Sequencing generated 984-101,293 reads per sample. Sequencing depth was strongly correlated with observed richness (R [2] = 0.808, p = 2 × 10[-7]). Comparisons of non-rarefied and rarefied datasets revealed no significant differences between early- and late-season nymphal ticks in observed richness, Shannon diversity, or Simpson diversity (all p > 0.05). In contrast, beta-diversity analyses identified significant differences in bacterial community membership between seasonal groups based on Jaccard dissimilarity (PERMANOVA: F = 1.5, R [2] = 0.066, p = 0.0102), whereas Bray-Curtis dissimilarity showed a non-significant trend toward seasonal separation (F = 2.2, R [2] = 0.090, p = 0.0834). Differential abundance analysis identified 18 amplicon sequence variants (ASVs) with raw p-values < 0.05, of which one Rickettsia-associated ASV remained significant following false discovery rate correction.

CONCLUSION: Seasonal differences in bacterial community composition were detected among nymphal ticks despite similar levels of microbial richness and alpha diversity. The enrichment of a Rickettsia-associated ASV in early-season ticks suggests that season may influence the occurrence of specific bacterial taxa within tick microbiomes. Further studies using higher-resolution sequencing and pathogen-specific approaches are needed to clarify the ecological significance of these seasonal patterns.},
}

@article {pmid42491558,
year = {2026},
author = {Gemeinholzer, B and Bonn, A and Ebert, B and Fischer, S and Güntsch, A and Holetschek, J and Johansson, VA and Friedrichs-Manthey, M and Röder, J and Schomburg, C and Steinthorsdottir, M and van Ommen Kloeke, E and de Boer, HJ},
title = {Experiences from national biodiversity data infrastructures in Europe: advancing data integration and community engagement.},
journal = {Bioscience},
volume = {76},
number = {7},
pages = {635-649},
pmid = {42491558},
issn = {0006-3568},
abstract = {The urgent need for comprehensive biodiversity data is driven by rapid biodiversity loss due to human activity. Drawing on insights from established national biodiversity data infrastructures in Europe, this article highlights eight key considerations for strengthening national data infrastructures-particularly in enhancing stakeholder engagement through improved data availability and accessibility. We emphasize the importance of collaboration among diverse stakeholders to enhance data sharing and integration. By utilizing technological advancements, implementing international standards for data interoperability under FAIR (Findable, Accessible, Interoperable, and Reusable) conditions, establishing robust communication strategies, and providing necessary training and legal guidance, these infrastructures can support effective data mobilization. Furthermore, promoting a culture of collaboration among stakeholders enhances the quality and applicability of biodiversity data for scientific research, policy, and conservation efforts. Our recommendations aim to ensure that national biodiversity data infrastructures effectively contribute to achieving the UN Global Biodiversity Framework targets and Sustainable Development Goals by encouraging strong partnerships and efficient data management practices.},
}

@article {pmid42496189,
year = {2026},
author = {Fernandes Erickson, M and Daluwatta Galappaththige, HSS and Mclean, DJ and Silva, DJA and Fulham, M and Wild, Z and Kelly, MBJ and Irving, CJ and Carlesso, D and Binns, GE and Silvasti, SA and Hämäläinen, L and O'Neill, LG and L'Herpiniere, K and Mappes, J and Kikuchi, DW and Rowland, HM and Power, M and White, TE and Kemp, DJ and Herberstein, ME},
title = {OzButterflies - a high quality open database of multispectral images and spectra of tropical to temperate Australian butterflies.},
journal = {Database : the journal of biological databases and curation},
volume = {2026},
number = {},
pages = {},
pmid = {42496189},
issn = {1758-0463},
support = {DP220102323//Australian Research Council/ ; FT170100417//Australian Research Council/ ; APSF22042//Australia and Pacific Science Foundation/ ; },
mesh = {Animals ; *Butterflies/genetics/anatomy & histology ; Australia ; *Databases, Factual ; Wings, Animal/anatomy & histology ; Female ; Male ; Electron Transport Complex IV/genetics ; },
abstract = {Butterflies have been a model system for studying the evolution of colour. This is partly due to their complex patterns that reflect human-visible (VIS) and ultraviolet (UV) light, which are perceived by conspecifics and predators. Many studies have sourced data from publicly available images, but most of these images only consider the visible spectrum of light. Including the UV spectrum is crucial for fully understanding the evolution of butterfly morphology and behavioural ecology. Here we provide standardized images (VIS and UV) of over 4 000 individuals from 16 communities of Australian butterflies. These communities represent different climates and urbanization levels spanning over 2 500 km. The dataset contains at least one individual of 125 different species from five families, constituting over one quarter of Australian butterfly diversity. In addition to photographs, we provide spectral measurements of butterfly wings for at least one individual of each species and sex, and Cytochrome Oxidase subunit 1 (CO1) sequences of 1 635 individuals. All these data are accessible in Zenodo and an associated R package simplifies the download of subsets of the database. This database will be of use to evolutionary biologists and ecologists interested in a broad range of topics related to phenotypic variation.},
}

Animals
*Butterflies/genetics/anatomy & histology
Australia
*Databases, Factual
Wings, Animal/anatomy & histology
Female
Male
Electron Transport Complex IV/genetics

@article {pmid42190858,
year = {2026},
author = {Qiu, J and Guo, X and Fan, G and Xu, H and Zhao, X and Xu, J},
title = {Integrated transcriptomic and metabolomic analysis of the toxic effects of PE microplastics on the Kumamoto oyster (Crassostrea sikamea).},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {308},
number = {},
pages = {110586},
doi = {10.1016/j.cbpc.2026.110586},
pmid = {42190858},
issn = {1532-0456},
mesh = {Animals ; *Transcriptome/drug effects ; *Microplastics/toxicity ; *Crassostrea/drug effects/metabolism/genetics ; Metabolomics ; Oxidative Stress/drug effects ; *Water Pollutants, Chemical/toxicity ; *Polyethylene/toxicity ; Hepatopancreas/drug effects/metabolism ; Multiomics ; Metabolome/drug effects ; Particle Size ; Biomarkers/metabolism ; },
abstract = {Microplastic pollution, particularly from polyethylene (PE), poses an increasing threat to coastal ecosystems, yet how particle size and exposure duration jointly regulate organismal responses remains poorly understood. Here, we investigated the size- and time-dependent toxic effects of PE-MPs (10 μm and 50 μm) on the Kumamoto oyster (Crassostrea sikamea) using an integrative framework combining physiological biomarkers (SOD, CAT, MDA), histopathology (gills and hepatopancreas), transcriptomics (gills), and metabolomics (hepatopancreas) during acute (1 day), short-term (7 days), and long-term (14 days) phases. Both PE-MP sizes induced significant oxidative stress and tissue injury in a time-dependent manner, with smaller particles casing more persistent oxidative stress, greater metabolic disturbance, and stronger immune suppression. Multi-omics analyses revealed a clear phase-dependent response pattern characterized by early defense activation, short-term metabolic reprogramming, and long-term functional suppression. Acute exposure activated oxidative stress responses, cytoskeletal remodeling, and particle clearance-related pathways, whereas short-term exposure was associated with metabolic reprogramming characterized by enhanced glycolysis and amino acid metabolism, suggesting increased energetic demands during stress responses. In contrast, long-term exposure resulted in coordinated suppression of immune, digestive, and lipid metabolic-related pathways, together with a metabolic shift toward long-term energy conservation. Overall, these findings suggest that PE-MPs exposure may induce coordinated physiological and metabolic adjustments associated with energy trade-offs under chronic stress conditions, highlighting the importance of particle size and exposure duration in ecological risk assessment for coastal and aquaculture environments.},
}

Animals
*Transcriptome/drug effects
*Microplastics/toxicity
*Crassostrea/drug effects/metabolism/genetics
Metabolomics
Oxidative Stress/drug effects
*Water Pollutants, Chemical/toxicity
*Polyethylene/toxicity
Hepatopancreas/drug effects/metabolism
Multiomics
Metabolome/drug effects
Particle Size
Biomarkers/metabolism

@article {pmid42475529,
year = {2026},
author = {Biondi, L and Gomes, N and Maior, RS and Silva, F and Silva, S and Soares, SC},
title = {Ecological context modulates the visual detection advantage for snakes.},
journal = {Cognition & emotion},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/02699931.2026.2697201},
pmid = {42475529},
issn = {1464-0600},
abstract = {Research indicates that the human visual system is highly efficient at detecting snakes, yet less is known about how ecological visual contexts modulate this advantage. We conducted two experiments with university students (N = 58 each) to test whether background complexity influences snake-detection efficiency using a dual-task paradigm. In Experiment 1, stimuli were presented on a uniform grey background. Here, snakes were detected and visually fixated significantly faster than non-snake control animals, consistent with previous findings. Crucially, this advantage was not influenced by participants' self-reported fear of snakes or anxiety levels. In Experiment 2, the same stimuli were embedded in a complex leaf-litter background. Under these conditions, non-snake stimuli were detected earlier than snakes, and overall accuracy declined. This indicates that the snake detection advantage is sensitive to changes in perceptual and contextual conditions, which may attenuate or reverse the pattern observed under simplified settings. Subjective fear scores again showed no moderating effect. Overall, these findings are consistent with an evolved sensitivity to snake-related visual features, but show that this advantage is context-dependent and can be attenuated or even reversed under ecologically complex visual conditions, independently of self-reported fear. They underscore the necessity of incorporating ecological variables into threat-detection research.},
}

@article {pmid42475681,
year = {2026},
author = {Li, R and Wu, W and Yan, C and Li, JT},
title = {CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.},
journal = {Nucleic acids research},
volume = {54},
number = {14},
pages = {},
pmid = {42475681},
issn = {1362-4962},
support = {2023YFF1304800//National Key Program of Research and Development, Ministry of Science and Technology of China/ ; 32370449//National Natural Science Foundation of China/ ; 32400407//National Natural Science Foundation of China/ ; 32570585//National Natural Science Foundation of China/ ; 32270449//National Natural Science Foundation of China/ ; 32325011//National Natural Science Foundation of China/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 2026NSFSCZY0073//Sichuan Science and Technology Program/ ; 2025ZYD0163//Sichuan Science and Technology Program/ ; },
mesh = {*Algorithms ; Animals ; Humans ; *Conserved Sequence/genetics ; *Software ; Evolution, Molecular ; *Genomics/methods ; Phylogeny ; Sequence Alignment ; Genome ; Computational Biology/methods ; },
abstract = {Conserved non-coding elements (CNEs) are fundamental components of gene regulatory networks in eukaryotes, yet their reliable identification across large-scale genomes and systematic evaluation of their genetic variation remains technically challenging, limiting comprehensive insights into their functional roles. To address these challenges, CNEwrap (https://github.com/YanCCscu/CNEwrap) was developed as a streamlined and modular bioinformatics toolkit that integrates subprograms capable of performing diverse tasks ranging from whole-genome alignment to CNE scanning and accelerated evolution analysis. Designed for high-throughput, multi-species applications, CNEwrap enables efficient and accurate discovery of genome-wide CNEs and comparative analysis of their variation across diverse taxa. Specifically, we developed a novel algorithm, "EvoAcc," designed for assessing accelerated evolution of specific species in different scenarios from CNE alignments. The EvoAcc algorithm integrates nucleotide variation frequencies and phylogenetic relationships to reconcile global conservation with clade-specific divergence, outperforming PhyloAcc, PhyloP, and ForwardGenomics in simulated datasets, particularly in scenarios involving two or three accelerated lineages. In validation analyses of functional genomic fragments across mammal species, EvoAcc performed comparably to existing algorithms in detecting human-specific accelerated segments while exhibiting superior sensitivity for InDel mutations and recovering specific signals missed by other algorithms. Case studies further confirm that CNEwrap is broadly applicable within diverse evolutionary lineages. Collectively, the CNEwrap pipeline establishes a scalable and integrative framework for uncovering CNEs and their evolutionary dynamics, while the incorporated EvoAcc algorithm complements existing methodologies, deepening insights into conserved regulatory architectures across eukaryotic evolution.},
}

*Algorithms
Animals
Humans
*Conserved Sequence/genetics
*Software
Evolution, Molecular
*Genomics/methods
Phylogeny
Sequence Alignment
Genome
Computational Biology/methods

@article {pmid42476159,
year = {2026},
author = {, },
title = {Global, regional, and national burden of road injuries 1990-2023: a systematic analysis for the Global Burden of Disease Study 2023.},
journal = {The Lancet. Public health},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2468-2667(26)00141-6},
pmid = {42476159},
issn = {2468-2667},
abstract = {BACKGROUND: Road injuries are a leading cause of mortality and morbidity worldwide. Years of international efforts have aimed to strengthen policy engagement, including the 2020 UN General Assembly's proclamation of the Second Decade of Action for Road Safety (2021-30), targeting a 50% reduction in road traffic deaths and serious injuries by 2030. The aim of this study is to provide estimates to monitor progress and identify intervention gaps.

METHODS: As part of the Global Burden of Diseases, Injuries, and Risk Factors Study 2023, we estimated incidence, mortality, and morbidity of road injuries for 204 countries and territories from 1990 to 2023. Four road injury types and 47 nature-of-injury categories were examined. Morbidity and mortality data from clinical records, vital registration, and police reports were harmonised using meta-analytic techniques to ensure consistency and correct for systematic bias. Incidence was modelled with the meta-regression tool Disease Modelling-Meta-Regression version 2.1 and cause-specific mortality with the Cause of Death Ensemble model, both incorporating location-specific covariates to support interpolation. Years of life lived with disability (YLDs) were estimated from the prevalence and severity of the nature of road injury, and years of life lost (YLLs) from the number of cause-specific deaths multiplied by the standard life expectancy at the age of death. Disability-adjusted life-years (DALYs) were the sum of YLLs and YLDs. All metrics were calculated with 95% uncertainty intervals (UIs).

FINDINGS: In 2023, there were 50·9 million (95% UI 46·1-56·1) road injury incident cases, 1·34 million (1·04-1·58) deaths, and 75·3 million (59·8-89·2) DALYs globally. Road injuries were the leading global cause of death among males aged 10-39 years. Between 1990 and 2023, age-standardised incidence decreased by 38·3% (95% UI 36·9-39·7) and mortality decreased by 32·3% (6·1-49·0), but progress varied widely by World Bank income group. Mortality in low-income countries (43·8 [95% UI 31·7-56·0] deaths per 100 000 population) was approximately six times higher than in high-income countries (7·5 [7·1-7·9] deaths per 100 000), despite the high-income countries showing the highest age-standardised incidence rates (858·1 [95% UI 781·9-947·1] cases per 100 000). In the past decade, many countries achieved notable reductions in road injuries, but others, including Ghana and the USA, saw increases. More severe injuries tended to occur in low-income and middle-income countries.

INTERPRETATION: Although global incidence, mortality, and DALY rates from road injuries have declined, progress remains uneven, with pronounced disparities across income groups reflecting systemic inadequacies in infrastructure, vehicle standards, enforcement, and post-crash care. Strengthening emergency response, improving road design, enforcing safety measures, and adapting policies to the evolving demographics remain essential.

FUNDING: Gates Foundation.},
}

@article {pmid42484728,
year = {2026},
author = {Karbasi, G and Ahmad, SA and Moradi, G and Danaee, M and Ishak, NH and Kunasekaran, P and Mohtar, MN},
title = {Validation of an mHealth adoption questionnaire for osteoporosis management in Iranian older adults at risk.},
journal = {Archives of osteoporosis},
volume = {21},
number = {1},
pages = {},
pmid = {42484728},
issn = {1862-3514},
mesh = {Humans ; *Osteoporosis/therapy ; *Telemedicine ; Surveys and Questionnaires ; Female ; Iran ; Aged ; Male ; Middle Aged ; Psychometrics ; Reproducibility of Results ; Digital Health ; Self Efficacy ; Health Literacy ; },
abstract = {BACKGROUND: With the increasing prevalence of osteoporosis among older adults and the growing need for effective self-management strategies, mobile health (mHealth) technologies may play an important role in supporting osteoporosis management. This study aimed to adapt and validate a culturally appropriate Persian questionnaire to assess mHealth adoption for osteoporosis management among Iranian adults aged ≥50 years, regardless of osteoporosis diagnosis status.

METHODS: A questionnaire was adapted from established theoretical frameworks, including the Unified Theory of Acceptance and Use of Technology (UTAUT), the Health Belief Model (HBM), self-efficacy, digital literacy, and technology anxiety. The instrument underwent cross-cultural adaptation and psychometric evaluation in two phases: (1) content validation and cognitive testing, and (2) construct validation using exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) with SmartPLS version 4.

RESULTS: The final instrument consisted of 54 items after removing poorly performing indicators. The measurement model demonstrated satisfactory psychometric properties, with average variance extracted (AVE) values ranging from 0.608 to 0.833 and composite reliability (CR) values between 0.866 and 0.950. Discriminant validity was supported by heterotrait-monotrait ratio (HTMT) values below the recommended threshold. Performance expectancy, self-efficacy, digital literacy, and perceived severity emerged as key determinants of mHealth adoption among older adults.

CONCLUSION: This study developed a culturally adapted Persian questionnaire with strong reliability and validity for assessing mHealth adoption in osteoporosis management among older adults. The instrument may help researchers, clinicians, and policymakers identify barriers to digital health engagement and design targeted interventions to improve mHealth adoption in ageing populations. The study designed and validated a culturally appropriate questionnaire to assess the acceptance of mHealth for osteoporosis management in Iranian adults over 50. Key predictors included performance expectancy, self-efficacy, and digital literacy. The findings support implementing tailored interventions to increase mHealth acceptance among older adults in resource-limited settings.},
}

Humans
*Osteoporosis/therapy
*Telemedicine
Surveys and Questionnaires
Female
Iran
Aged
Male
Middle Aged
Psychometrics
Reproducibility of Results
Digital Health
Self Efficacy
Health Literacy

@article {pmid40913400,
year = {2026},
author = {Zhong, H and Shi, Y and Kozlova, A and Moravcova, R and Rogalski, JC and Jamieson, A and Lansing, L and Moon, KM and Yuan, X and Gregoris, AS and Higo, H and Common, J and Conflitti, IM and Pepinelli, M and Tran, L and Cunningham, M and Jabbari, H and Bukhari, SA and French, SK and Polo, RO and Hoover, SE and Pernal, SF and Giovenazzo, P and Guarna, MM and Zayed, A and Foster, LJ},
title = {Omics Insights Into the Effects of Highbush Blueberry and Cranberry Crop Agroecosystems on Honey Bee Health and Physiology.},
journal = {Proteomics},
volume = {26},
number = {8},
pages = {41-57},
doi = {10.1002/pmic.70033},
pmid = {40913400},
issn = {1615-9861},
support = {AAFC J-002368//Government of Canada through Agriculture and Agri-Food Canada (AAFC) Genomics Research and Development Initiative (GRDI)/ ; LSARP #16420//Genome Canada/ ; OGI-185//Ontario Genomics Institute/ ; 374PRO//Life Sciences Institute, and Genome BC/ ; },
mesh = {Animals ; Bees/physiology/microbiology ; *Blueberry Plants ; Multiomics ; *Vaccinium macrocarpon ; Proteomics/methods ; Gastrointestinal Microbiome ; Agroecology ; Crops, Agricultural ; },
abstract = {Honey bees (Apis mellifera) are vital pollinators in fruit-producing agroecosystems like highbush blueberry (HBB) and cranberry (CRA). However, their health is threatened by multiple interacting stressors, including pesticides, pathogens, and nutritional changes. We tested the hypothesis that distinct agricultural ecosystems-with different combinations of agrochemical exposure, pathogen loads, and floral resources-elicit ecosystem-specific, tissue-level molecular responses in honey bees. We conducted an integrated multi-omics analysis using RNA-sequencing (RNA-seq), proteomics, and gut microbiome profiling across three key tissue types (head, abdomen, and gut) of honey bees collected from two agroecosystems over two field seasons. Quantification was performed for pesticide residues, pathogen loads (Nosema spp., Varroa destructor, and multiple viruses), and gut microbiota. Weighted gene co-expression network analysis (WGCNA) revealed tissue-specific protein modules with ecosystem-associated patterns, which differed from RNA co-expression networks. Microbiome composition also varied, with key genera like Gilliamella, Snodgrassella, and Bartonella correlating with metabolic modules. These findings underscore the complex, environment-dependent impacts of agroecosystem conditions on bee health. Our study provides a system-level understanding of how combined pesticide, pathogen, and parasitic stressors, mediated by diet and microbiome, shape molecular phenotypes in honey bees-informing strategies for pollinator protection in managed landscapes. SUMMARY: This study provides a comprehensive multi-omics analysis of honey bees foraging in blueberry and cranberry agroecosystems, offering novel insights into the molecular mechanisms underlying pollinator health in managed crop environments. By integrating transcriptomic, proteomic, and microbiome profiling across key tissues-head, abdomen, and gut-we reveal how environmental stressors, including pesticide exposure, pathogen infections, and parasitic infestations (e.g., Varroa destructor), differentially impact bee physiology and microbiome composition. Our findings highlight tissue-specific responses to these stressors, with distinct metabolic pathway alterations observed in each tissue. Proteomic and transcriptomic analyses uncovered dysregulated pathways linked to oxidative phosphorylation and protein synthesis, while microbiome analysis revealed crop-dependent shifts in gut bacterial communities, suggesting potential roles in pesticide detoxification and immune modulation. Notably, we identified key molecular biomarkers associated with stress adaptation, which may serve as early indicators of colony health deterioration. This research underscores the need for a system-level approach to understanding pollinator stress in agricultural landscapes. By elucidating the interactions between diet, pesticide residues, pathogen loads, and molecular stress responses, our study provides a foundation for targeted conservation strategies aimed at mitigating environmental risks and improving pollination sustainability in agroecosystems.},
}

Animals
Bees/physiology/microbiology
*Blueberry Plants
Multiomics
*Vaccinium macrocarpon
Proteomics/methods
Gastrointestinal Microbiome
Agroecology
Crops, Agricultural

@article {pmid42407216,
year = {2026},
author = {Zhang, B and Wang, X and Kuang, C and Wu, J and Hong, Y},
title = {Development of an integrated workflow (NosZRef) for rapid and accurate nosZ gene profiling and its application to oceanic ecosystems.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108247},
doi = {10.1016/j.marenvres.2026.108247},
pmid = {42407216},
issn = {1879-0291},
mesh = {Workflow ; *Ecosystem ; High-Throughput Nucleotide Sequencing ; Nitrous Oxide/metabolism ; Oceans and Seas ; *Bacteria/genetics ; Gene Expression Profiling ; Computational Biology ; },
abstract = {The widespread adoption of next-generation sequencing technologies and the rapid growth of publicly available sequence data have generated an unprecedented resource for investigating nitrous oxide (N2O) reducing microorganisms. However, the lack of standardized practices has hindered cross-study comparisons and limited our ability to thoroughly assess the community structure, diversity and biogeography of N2O-reducing microorganisms. To address these knowledge gaps, a bioinformatic workflow was developed to standardize the processing of nosZ gene datasets originating from high-throughput sequencing. We first manually curated and constructed a comprehensively annotated reference protein sequence database containing 3,361, 5,665, and 96 sequences from the NosZ-I, NosZ-II, and NosZ-III clades, respectively. Integrated with this database, we developed NosZRef, a fast, accurate and scalable analytical pipeline for nosZ gene profiling. With one single command, NosZRef provides users full-pipeline analysis from raw reads to statistical and visualization outputs. We employed NosZRef to profile nosZ genes across diverse depths in the Tara Oceans dataset, revealing that the three nosZ clades exhibit distinct depth-dependent distribution patterns and ecological strategies. In summary, NosZRef offers high specificity and comprehensive coverage for accurate profiling of N2O-reducing microorganisms in oceanic ecosystems from high-throughput sequencing data, providing a useful tool for investigating microbially mediated N2O reduction in oceanic environments. NosZRef is available at https://github.com/ZhangBaoshan668/NosZRef.},
}

Workflow
*Ecosystem
High-Throughput Nucleotide Sequencing
Nitrous Oxide/metabolism
Oceans and Seas
*Bacteria/genetics
Gene Expression Profiling
Computational Biology

@article {pmid42429456,
year = {2026},
author = {Flamholz, ZN and Mulay, SA and Leshyk, V and Caporaso, JG and Eisen, JA and Kelly, L and Lloyd, KG and Osburn, MR and Podar, M and Roux, S and Regberg, SAB and Ruff, SE and Tierney, B and Tighe, S and Trembath-Reichert, E and Venkateswaran, K and Woyke, T and Locken, KM and Sapers, HM and Whiteson, K},
title = {Exploring life's hidden majority: microbial dark matter symposium highlights.},
journal = {mSphere},
volume = {11},
number = {7},
pages = {e0058725},
pmid = {42429456},
issn = {2379-5042},
mesh = {Metagenomics ; *Microbiota ; Bacteria/genetics/classification ; Computational Biology ; Ecosystem ; },
abstract = {The Microbial Dark Matter Symposium held on August 28-29, 2025, in Laguna Beach, Orange County, CA, convened a multidisciplinary group of scientists to address the vast unknowns in microbial life-from uncultured taxa and uncharacterized proteins to elusive viruses and spacefaring microbes. Set against a scenic coastal backdrop, the symposium highlighted advances in single-cell genomics, proximity ligation sequencing, and artificial intelligence-ready bioinformatics, while also probing the limits of microbial persistence, metabolism, and ecological distribution. Sessions explored microbial dark matter from multiple dimensions: cultivability, where new strategies are enabling recovery of elusive microbes; functional ambiguity, where metagenomic dark zones are illuminated by computational annotation; and genomic representation, where single-cell methods bridge gaps left by shotgun community sequencing. Researchers shared breakthroughs in identifying atmospheric microbiomes, "dark oxygen" production in groundwater ecosystems, and microbial survival on the International Space Station. The symposium emphasized integration of methods, disciplines, and ecosystems, advancing a collective push to illuminate the microbial dark matter on Earth and beyond. By highlighting emerging tools, pressing questions, and cross-domain insights, the symposium underscored the need for collaborative, open, and adaptive approaches to study the microbial unknown. The meeting marks a pivotal moment in microbiology, where cultivating knowledge of the uncultivated promises transformative understanding of life, everywhere.},
}

Metagenomics
*Microbiota
Bacteria/genetics/classification
Computational Biology
Ecosystem

@article {pmid42465418,
year = {2026},
author = {Sharma, J and Maldonado, B and Ungar, R and Adimoelja, A and Flores, JP and Gjorgjieva, T and Jones, K and Khan, A and Xue, D and Patel, R and Caggiano, C},
title = {Recommendations for the ethical and accurate use of population descriptors: a trainee-led survey of early-career researchers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42465418},
issn = {2692-8205},
abstract = {Despite the importance of population descriptors in human genomics research, many scientists struggle to translate evolving ethical guidelines into their computational workflows. To characterize this gap between recommendations and implementation, we conducted a mixed-methods survey of early-career researchers to assess how they understand and implement the landmark 2023 NASEM report on the use of population descriptors in human genetics research. We show that while exposure to the report fosters ethical awareness, fundamental misconceptions about race and ancestry persist across academic disciplines, and trainees face structural bottlenecks, including legacy data constraints and a lack of technical confidence. To address this gap, we offer actionable, stakeholder-specific recommendations across the research lifecycle ranging from decision-support tools to "bring-your-own-data" workshops to leadership from academic journals, scientific societies, and trainee mentors. Ultimately, we argue that to promote scientific rigor and reduce bias in genetic discoveries, the scientific ecosystem must invest in the infrastructure necessary to empower the next generation of researchers.},
}

@article {pmid42470576,
year = {2026},
author = {Kamp, K and Yoo, L and Kale, T and Zhang, X and Malloy, C and Kahveci, I and Cordova, R and Hernandez, I and Tsai, CS and Pan, TD and Clark-Snustad, K and Lee, S and Levy, RL and Keefer, L and Heitkemper, M},
title = {Feasibility, Acceptability, and Preliminary Effects of a Nurse-Delivered Self-Management Program for Individuals with Inflammatory Bowel Disease: A Pilot Randomized Controlled Trial.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42470576},
issn = {1573-2568},
support = {K23 NR020044/NR/NINR NIH HHS/United States ; P2C HD042828/HD/NICHD NIH HHS/United States ; T32016913/NR/NINR NIH HHS/United States ; UL1 TR002319/TR/NCATS NIH HHS/United States ; },
abstract = {PURPOSE: Individuals with inflammatory bowel disease experience persistent symptoms and disease challenges which may not be solved with medical management. Self-management interventions may support patients, but their feasibility, acceptability, and preliminary effectiveness should be evaluated prior to large-scale testing.

METHODS: We conducted a pilot randomized controlled trial with 2:1 allocation of a nurse-delivered, self-management program to usual care. Adults with a healthcare provider diagnosis of ulcerative colitis or Crohn's disease, aged 18-75 years, currently reporting at least two symptoms were recruited. The self-management program included eight online modules plus weekly phone check-ins with a registered nurse. Feasibility and acceptability were measured using surveys and interviews. Secondary outcomes included patient activation, self-regulation, self-efficacy, functional impairment, quality of life, symptoms, and fecal calprotectin. Linear mixed models estimated the differences in change scores between groups from baseline to 3- and 6-month follow-up.

RESULTS: Fifty-five participants were randomized (n = 36 self-management, n = 19 usual care). Participants were on average 39.0 years old (range: 20-73), 76.4% women, and 80% Crohn's disease. The self-management program demonstrated high satisfaction (91.1/100), feasibility (4.34/5), and acceptability (4.28/5). Compared with usual care, the self-management program produced the largest improvement in functional impairment (mean change - 15.1 [95% CI - 23.3, - 6.8], with additional improvements in patient activation (10.3 [2.8, 17.9]), self-regulation (4.1 [1.1, 7.1]), and quality of life (4.6 [0.3, 8.9]). Symptom severity and fecal calprotectin were largely unchanged. Qualitative feedback emphasized the value of regular nurse check-ins, accountability, and applicability of the program beyond disease-specific concerns.

CONCLUSIONS: A nurse-delivered self-management program was feasible, acceptable, and led to meaningful changes in key intervention targets for inflammatory bowel disease management. High engagement supports potential for future testing in a fully powered trial and eventual integration into routine care.},
}

@article {pmid42470863,
year = {2026},
author = {Guan, Q and Ji, P and Guan, C and Chen, A and Tang, X and Wang, Y and Gong, T and Guo, K},
title = {A framework for constructing water ecological security patterns based on water provision service flow simulation.},
journal = {Journal of environmental management},
volume = {414},
number = {},
pages = {130488},
doi = {10.1016/j.jenvman.2026.130488},
pmid = {42470863},
issn = {1095-8630},
abstract = {Constructing a Water Ecological Security Pattern (WESP) is essential for mitigating water scarcity, yet existing methods are mostly based on static supply-demand assessments and fail to capture the spatial flow pathways of water resources between supply and demand areas. This results in WESPs lacking spatial connectivity and process integrity. To address these gaps, this study quantifies the supply and demand of water provision service and proposes a network model-based simulation approach for water provision service flows. The proposed method integrates the Least Cost Path (LCP) model with an Iterative Dynamic Allocation algorithm, enabling the joint consideration of landscape resistance and human demand in simulating the dynamic flow process of water provision service. The simulation results are used to identify key spatial elements for WESP construction in the Yellow River Delta (YRD), thereby providing a basis for establishing a WESP with dynamic connectivity. Analysis across three representative years indicates a persistent water deficit in the YRD. A growing spatial mismatch was observed, driven by declining supply in the north and surging demand in the south. The simulated flow network demonstrates a distinct "periphery-to-center" convergence, connecting coastal supply nodes to inland demand centers through 62 key flow pathways. Based on these dynamics, we proposed a WESP comprising "five zones, two corridors, three belts, and three cores". According to its structural characteristics, these spatial elements are further classified into four management zones, for which differentiated spatial regulation strategies are developed. These findings offer a novel, flow-based perspective for resolving supply-demand imbalances and enhancing regional water security.},
}

@article {pmid42471340,
year = {2026},
author = {Zeng, F and Song, C and Woolway, RI and Ke, L and Wang, J and Feng, D and Allen, GH and Lin, P and Liu, K and Chen, T and Zhan, P and Fan, C and Zhang, H and Huang, L and Pavelsky, TM},
title = {Human imprints on global riverfronts.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75777-0},
pmid = {42471340},
issn = {2041-1723},
abstract = {Rivers are profoundly shaped by human activity along their water-land interfaces (riverfronts), yet the global distribution and drivers of these imprints remain poorly understood. Here we present a high-resolution global map of 7.52 million kilometers of riverfronts using satellite imagery and deep learning. We find that nearly 20% of global riverfronts are anthropogenically modified, primarily by agriculture (13.43%) and built-up areas (6.29%). A distinct modification belt spans parts of Africa and Eurasia, accounting for ~60% of global alterations, with imprint densities six times higher than elsewhere. This lateral fragmentation represents a pervasive human pressure that differs fundamentally from dam-induced longitudinal fragmentation, and is closely linked to deteriorating water quality and biodiversity threats. Environmental constraints and region-specific socio-economic dependencies further shape these spatial patterns. Our findings inform riverfront management and underscore the urgent need to reconcile development with the ecological integrity of these transitional zones.},
}

@article {pmid42473400,
year = {2026},
author = {Wang, Q and Xing, XT and Meng, F and Liu, PD and Liu, Y and Yang, Y and Huo, AD},
title = {[Prediction of Land Use and Ecological Network in Shandong Province by Coupling SD-PLUS-InVEST Model].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {7},
pages = {4846-4857},
doi = {10.13227/j.hjkx.202506065},
pmid = {42473400},
issn = {0250-3301},
abstract = {Under the background of "double carbon，" it is of great significance to study the land use change in Shandong Province to maintain the security of the ecosystem and build a sustainable ecological network. Based on the analysis of land use data in 2010 and 2020， this study coupled the SD-PLUS model to simulate the land use evolution in 2030 and 2060 under three scenarios in CMIP6： low emission sustainable development scenario （SSP119）， medium emission baseline scenario （SSP245）， and high emission extreme scenario （SSP585）， and we then extracted the land use pattern. The InVEST model was used to evaluate the habitat quality， and the MSPA model and MCR model were further combined to construct the ecosystem network of Shandong Province. The results show that： ① From 2010 to 2020 （historical period）， land use was dominated by cultivated land but continued to decrease， with the dual-core expansion of construction land， the slight growth of forest land and water area， and the continuous reduction of grassland and unused land. From 2020 to 2060 （the future period）， under the SSP119 scenario， the cultivated land area will decrease to 64.01 %， the construction land will increase to 25.37 %， the forest land and water area will increase， and the grassland and unused land area will decrease. Under the SSP585 scenario， the decrease of cultivated land was the largest， and the proportion of construction land was the highest in the three scenarios. ② Changes in habitat quality： In the historical period， the pattern of "high in the east and low in the west" was presented， and the contribution of cultivated land was > 60 %. Under the SSP119 scenario in the future period， the high-value areas of mountainous and coastal areas in the central and western regions will be optimized， and the contribution of forest habitat will be the most obvious. Under the SSP245 scenario， the habitat in southwest Shandong Province and the Yellow River Delta was degraded and partially fragmented. Under the SSP585 scenario， the habitat quality in the plain area was degraded in a large area， and the contribution of various habitats decreased. ③ Ecological network construction： From 2010 to 2020， the ecological source area developed into the "East-Central-South" three poles， and the ecological network was gradually optimized. In the future， under the SSP119 scenario， the mountainous areas of central Shandong Province and Jiaodong Peninsula will form a dense network， and the corridors will be interwoven and connected. Under the SSP245 scenario， a buffer zone appears in the northwestern Shandong Plain， and the secondary corridor expands， but the Jiaoji Economic Belt is still dominated by the primary corridor. In the context of SSP585， the ecological source is fragmented， and the first-level corridor along Jiaoji is the core， and there are only sparse low-level corridors in southwestern Shandong Province.},
}

@article {pmid42475117,
year = {2026},
author = {Alexsandra, N and Mazaya, M and Prawira, AY and Surya Alwi, R},
title = {Molecular modeling of the stability of the interaction of Sunda porcupine (Hystrix javanica) quill protein homologs with vascular endothelial growth factor receptor 2 (VEGFR-2).},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07391102.2026.2702491},
pmid = {42475117},
issn = {1538-0254},
abstract = {Porcupines (Hystrix spp.) are widely distributed rodents known not only for their ecological roles but also for their traditional medicinal applications. In Indonesia, quills from species like Hystrix javanica, Hystrix sumatraensis, and Hystrix brachyura are traditionally used to relieve pain and promote wound healing. Scientific studies have revealed that porcupine quills are rich in bioactive compounds, including keratin, peptides, flavonoids, and triterpenoids. Keratin, a structural protein abundant in epithelial cells extracted from porcupine quill, has been found to support various wound-healing processes, having antibacterial properties, and the ability to induce apoptosis in breast cancer cells. Meanwhile, the vascular endothelial growth factor receptor 2 (VEGFR-2) plays a crucial role in angiogenesis and tissue regeneration during the wound-healing process. This study employed exploratory structural bioinformatics to study the potential interaction between porcupine quill-derived homolog proteins and VEGFR-2 from our previous published work. Through protein-protein docking and molecular dynamics simulation, we predicted molecular recognition and binding affinity computationally. Keratin type II (P50446), Krt2 (B2RTP7), and Keratin isoform X1 (A0A6P5R3S8) demonstrated the most robust and stable interactions with VEGFR-2. Contrarily, Keratin type II (P04264) displayed comparatively greater structural fluctuations and weaker stability, suggesting less optimal and more flexible binding interactions with the receptor. Thus, this research provides preliminary hypothesis evidence of potential interactions between porcupine quill-derived proteins and VEGFR-2, supporting further experimental studies to determine whether these interactions have biological relevance in wound-healing processes.},
}

@article {pmid42475360,
year = {2026},
author = {Duane, D and Duggan, MT and Berlik, E and Dantzker, MS and Rice, AN and Freeman, LA},
title = {Multi-class, unsupervised detection and classification of biological and anthropogenic sounds in coral reefs.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014516},
pmid = {42475360},
issn = {1553-7358},
mesh = {*Coral Reefs ; Animals ; Classification Algorithms ; *Unsupervised Machine Learning ; Acoustics ; Sound Spectrography/methods ; *Vocalization, Animal/classification/physiology ; Computational Biology ; Hawaii ; *Sound ; Autoencoder ; Clustering Algorithms ; Humans ; Environmental Monitoring/methods ; Anthropogenic Effects ; },
abstract = {Analyzing the complex and diverse soundscapes of ecosystems such as coral reefs remains a challenge for understanding environmental dynamics and processes. While machine learning techniques can significantly improve detection and classification capabilities, applications of traditional supervised learning to underwater acoustics are limited by the size and class-coverage of labeled datasets. Unsupervised machine learning offers the potential to detect and classify sounds without the guidance of human labels, including signals that were unknown to the human analyst. However, the majority of previously developed unsupervised approaches characterize reef soundscapes from correlative metrics without identifying specific sounds, and the few that detect individual signals have been trained on limited data (<10 days), which constrains the potential to generalize across datasets and geographical localities. Here, a convolutional autoencoder was built and trained on year-long acoustic datasets from four Hawaiian coral reefs, and latent embeddings were clustered using Gaussian mixture modeling. A total of 29 classes were automatically generated, and a manual review of samples in each class determined that nine of the classes corresponded to distinct biological and anthropogenic sounds. The classes were identified to be two call types from the damselfish, Dascyllus albisella, parrotfish feeding sounds, holocentrid calls, an unidentified fish sound, three humpback whale song units, and ship noise. The classifier was found to be robust against an independently-collected test dataset with D. albisella calls (AUC = 0.9) with no extra training on the labels. Diel, lunar, and seasonal trends were observed for all nine classes, including previously-unidentified responses of the holocentrid and unknown fish groups to lunar illumination. This work demonstrates the capability of unsupervised algorithms to cluster acoustic signals into identifiable biological and anthropogenic categories in order to examine and characterize ecological trends.},
}

*Coral Reefs
Animals
Classification Algorithms
*Unsupervised Machine Learning
Acoustics
Sound Spectrography/methods
*Vocalization, Animal/classification/physiology
Computational Biology
Hawaii
*Sound
Autoencoder
Clustering Algorithms
Humans
Environmental Monitoring/methods
Anthropogenic Effects

@article {pmid42462070,
year = {2026},
author = {Li, CY and Jiao, ZZ and Zhang, LQ and Li, H and Wang, MY and Guo, WH and Wang, YX and Wang, Y},
title = {Application of Just-in-Time Adaptive Interventions in Dietary Health Management: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e92139},
pmid = {42462070},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; Telemedicine ; Digital Media ; },
abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) use real-time data to deliver personalized support at moments of heightened need and may improve dietary behaviors in real-world settings.

OBJECTIVE: The aim of this study is to systematically review the application, characteristics, and effectiveness of JITAIs in dietary health management.

METHODS: We included human studies evaluating JITAIs-based dietary interventions delivered through digital platforms that used real-time or near-real-time data to tailor intervention content, timing, or intensity. Eligible studies reported at least one behavioral, engagement, physiological, or clinical outcome; reviews, protocols, editorials, commentaries, and studies without outcome data were excluded. We searched PubMed, Embase, Scopus, CINAHL, Web of Science, ClinicalTrials.gov, WHO ICTRP (International Clinical Trials Registry Platform), and ISRCTN (International Standard Randomized Controlled Trial Number) from inception. The initial search was conducted on August 20, 2025, and updated on March 16, 2026; reference lists were also screened manually. Two reviewers independently screened studies and extracted data. Methodological quality was assessed using the 2018 Mixed Methods Appraisal Tool, and reporting quality was assessed using the Mobile Health Evidence Reporting and Assessment checklist. Because of substantial heterogeneity, findings were synthesized narratively. The review was registered in PROSPERO (International Prospective Register of Systematic Reviews; CRD420261285292).

RESULTS: Twenty studies involving 2948 participants were included. Target populations comprised individuals with overweight or obesity, chronic conditions, and eating disorders and the general population engaged in dietary management. Interventions were mainly delivered via smartphone apps, SMS text messaging, wearable-device feedback, and context-triggered notifications. More consistent benefits were observed for proximal behavioral and process outcomes, including fruit and vegetable intake, sodium-restriction behaviors, drinking automaticity, self-monitoring, eating-related behaviors, and responsiveness to prompts. Some studies also reported improvements in distal clinical outcomes, such as body weight, BMI, waist circumference, blood pressure, blood glucose, and selected biochemical indicators. However, these findings were inconsistent, and most studies did not show clear between-group advantages. Common implementation barriers included device incompatibility, variability in digital literacy, geolocation or signal limitations, and burden from frequent prompts.

CONCLUSIONS: JITAIs-based dietary interventions appear promising for supporting timely and individualized dietary behavior change, particularly for proximal behavioral outcomes, although evidence for sustained clinical effects remains inconsistent. This review contributes to the JITAIs literature by examining dietary health management as a distinct application domain and by synthesizing evidence that has otherwise been dispersed across broader reviews of digital behavior change and weight management. By integrating intervention characteristics, delivery approaches, triggering mechanisms, and effects across diverse populations, it clarifies methodological and implementation gaps and informs more standardized intervention design and reporting. These findings support the development of scalable, context-sensitive digital dietary interventions for clinical care, chronic disease self-management, weight management, and public health nutrition.},
}

Humans
Digital Health
Telemedicine
Digital Media

@article {pmid42463295,
year = {2026},
author = {Chen, H and Wu, Y and Wang, X and Liang, D and Yang, Y and Xu, Y and Wu, W},
title = {Multi-Omics Reveal Extracellular Electron Transfer Mechanism Under Deep-Sea High Salinity.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70376},
pmid = {42463295},
issn = {1462-2920},
support = {25ZR1402191//Natural Science Foundation of Shanghai Municipality/ ; 52500086//National Natural Science Foundation of China/ ; 42106046//National Natural Science Foundation of China/ ; 42376047//National Natural Science Foundation of China/ ; },
mesh = {Electron Transport ; *Shewanella/metabolism/genetics ; *Salinity ; *Seawater/microbiology ; Multiomics ; Bacterial Proteins/genetics/metabolism ; Riboflavin/metabolism ; Citric Acid Cycle ; },
abstract = {Microorganism-mineral interaction is crucial for understanding the degradation of organic matter involved in the electron exchange in marine sediments. Widespread metal-reducing bacteria Shewanella spp. have a unique ability of extracellular electron transfer (EET); however, their EET activity and underlying mechanisms under high-salinity stress in the deep sea remain poorly explored. Here, we studied the EET process and the underlying metabolic mechanism based on a deep-sea bacterium Shewanella piezotolerans WP3. S. piezotolerans WP3 has comparable electroactivity to the model strain S. oneidensis MR-1, achieving a maximum current density of 9.7 ± 0.7 μA/cm[2] at 0.6 V vs. Ag/AgCl. Multiheme-cytochrome OmcA-MtrCAB complex contributed to the direct EET, with mtrB, mtrA and omcA-1 upregulated and the redundant omcA genes (i.e., omcA-4, omcA-3) exhibiting low expression. Riboflavin, synthesised from guanosine triphosphate under high-salinity conditions, was secreted to facilitate EET. Enhanced glycolysis and TCA cycle activities under high anode potential (0.6 V) were confirmed by the downregulation of intermediate metabolites (e.g., phosphoenolpyruvate) and the upregulation of corresponding genes (e.g., pyk), supporting the high energy yield for the EET process. Our findings provide new insights into the EET mechanisms of marine Shewanella, paving the way for the development of bioelectronic sensors and biotechnology applications in high-salinity wastewater.},
}

Electron Transport
*Shewanella/metabolism/genetics
*Salinity
*Seawater/microbiology
Multiomics
Bacterial Proteins/genetics/metabolism
Riboflavin/metabolism
Citric Acid Cycle

@article {pmid42463489,
year = {2026},
author = {Gao, Z and Wu, J and Lucaci, AG and Ouyang, J and Wang, L and Ryon, KA and Elhaik, E and Probst, AJ and Rodó, X and Velavan, TP and Chasapi, A and Ouzounis, CA and Oliveira, M and Dias-Neto, E and Osuolale, O and Poulsen, M and Meleshko, D and Bhattacharyya, M and Ugalde, JA and Tull, A and Rubins, KH and Sierra, MA and Tierney, BT and Prithiviraj, B and Sharma, NK and Munteanu, V and Mangul, S and Kurt, KC and Ushio, M and Mazur-Panasiuk, N and Kopera, K and Marszałek, K and Kowalski, M and Toscan, RB and Branicki, W and Pyrć, K and Łabaj, PP and Subramanian, B and Frolova, A and Burkhart, JG and Deng, Y and Udekwu, KI and Schriml, LM and Hazrin-Chong, NH and Suzuki, H and Lee, PKH and Camargo, AP and Kyrpides, NC and Liu, D and Wang, LF and Mason, CE and Shi, T and , },
title = {Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42463489},
issn = {2041-1723},
support = {32370720//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Cities ; Animals ; },
abstract = {RNA viruses represent an integral component of human-associated environments and human health. However, the ecology of environmental RNA viruses remains largely unexplored. Here, we analyzed 2922 metatranscriptomic samples collected from urban and surrounding environments-including human-dense settings (e.g., transit hubs, hospitals, banks), alongside peri-urban settings - across 102 cities in 31 countries and constructed the Urban & Peri-urban RNA Virus Atlas (UPVAtlas), comprising 54,945 RNA viruses, 77% of which had not been previously observed. Phylogenetic reconstruction based on RNA-dependent RNA polymerases from UPVAtlas greatly expanded the evolutionary diversity of RNA viruses, leading to the identification of two potential candidate phyla, one candidate class, and several unclassified clades. Host association analyses further revealed the ecological complexity of environmental RNA viruses, with the diversity of vertebrate-related and ESKAPE pathogen-related viruses underscoring the importance of continued monitoring of urban environments for tracking RNA viral prevalence and dynamics, with direct relevance to future public health.},
}

Humans
*Virome/genetics
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
RNA, Viral/genetics
Cities
Animals

@article {pmid42463898,
year = {2026},
author = {Siepe, BS and Haslbeck, JMB and Kloft, M and Büchner, A and Zhang, Y and Fried, EI and Heck, DW},
title = {Introducing openESM: A database of openly available experience sampling datasets.},
journal = {Behavior research methods},
volume = {58},
number = {8},
pages = {},
pmid = {42463898},
issn = {1554-3528},
support = {VENI grant number 221G.110//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWO gravitation grant number 024.004.016//Dutch Research Council and the Dutch Ministry of Education, Culture and Science/ ; European Union's Horizon 2020 research and innov//H2020 European Research Council/ ; Doctoral Scholarship//German Academic Scholarship Foundation/ ; },
mesh = {Humans ; *Databases, Factual ; *Ecological Momentary Assessment ; Internet ; },
abstract = {Experience sampling via mobile devices enables unprecedented insights into daily life. However, individual studies often cannot answer research questions conclusively, and open data are scattered across repositories in different formats. This impedes research into robustness, generalizability, and heterogeneity. We address this issue by introducing openESM, an open-source database of openly available experience sampling datasets in a harmonized format. The growing database currently comprises 60 datasets with more than 16,000 participants and more than 740,000 observations. Metadata can be searched via our website (openesmdata.org) to select and download datasets via packages in R and Python. We demonstrate the potential of openESM through an analysis of within-person correlations of positive and negative affect in 39 datasets, providing evidence for a large negative momentary correlation (- 0.49 , 95% CI: [ - 0.54 , - 0.42 ]). We end by discussing the design principles that will allow openESM to become a continuously evolving community resource for cumulative experience sampling research.},
}

Humans
*Databases, Factual
*Ecological Momentary Assessment
Internet

@article {pmid42465405,
year = {2026},
author = {Hunt, M and Torres, MDT and Alikhan, NF and Anderson, D and Andreani, ML and Blom, J and Bouras, G and Brinkman, FSL and Carroll, LM and Croxen, MA and Floto, RA and Hall, MB and Hawkey, J and Horsfield, ST and Jia, B and Lacey, JA and Lee, HS and Lima, L and MacAlasdair, N and Mallawaarachchi, S and Matlock, W and Moustafa, AM and Petit, R and Ramnath, V and Raghuram, V and Russell, MJ and Sanderson, T and Saratto, T and Schwengers, O and Seemann, T and Shaw, LP and Shen, W and Thomson, N and Tonkin-Hill, G and Toussaint, J and Viet, TL and von Wachsmann, J and Wan, F and Weimann, A and Wheatley, RM and Wiatrak, M and Xie, O and de la Fuente-Nunez, C and Lees, JA and Iqbal, Z},
title = {AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42465405},
issn = {2692-8205},
abstract = {Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not uniformly assembled, quality controlled, annotated or searchable at scale. Here we present AllTheBacteria, an open, community-built resource that transforms public bacterial short-read whole-genome sequencing reads into a uniformly processed discovery platform. The current analysed release contains 2,440,377 high-quality bacterial and archaeal genomes from 11,273 species, together with standardized taxonomic assignments, genome annotations, antimicrobial resistance calls, antiphage-defence annotations, protein structure predictions and AI-ready sequence tables. We show that this infrastructure enables applications that would otherwise be impractical, from global sequence search and outbreak contextualization to pangenome method development, antimicrobial resistance reservoir mapping and antiphage-defence ecology. As a stringent experimental demonstration, we mined 3,919,096 encrypted peptide fragments from AllTheBacteria proteomes using our deep learning model APEX 1.1, identifying 1,867 candidates with predicted antimicrobial activity. We synthesized 24 representative peptides and tested them against 20 clinically relevant bacterial strains, including antibiotic-resistant pathogens. Multiple peptides showed low-micromolar activity, membrane-responsive conformational transitions and selective envelope perturbation. A lead molecule, ATB20, reduced Acinetobacter baumannii burden in a murine skin abscess model with efficacy comparable to polymyxin B and no overt toxicity. Together, these results establish AllTheBacteria as both a foundational community resource for microbiology and a renewable engine for AI-guided antimicrobial discovery.},
}

@article {pmid42098178,
year = {2026},
author = {Brant, CO and Silvis, S and Bennion, DH and Castiglione, C and Tyrrell, K and Hannahs, K and Slattery, M and Bunnell, D and Honsey, A and Tingley, R and King, K and Alofs, KM and Ackiss, A and Bronte, CR and Smith, J and Herbert, M},
title = {Two hundred years of historical spawning and nursery data for coregonine fishes in the Laurentian Great Lakes.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42098178},
issn = {2052-4463},
mesh = {*Salmonidae ; *Lakes ; *Conservation of Natural Resources ; Ecosystem ; Great Lakes Region ; Databases, Factual ; Species Specificity ; Animals ; },
abstract = {Historical data can provide critical ecological information for species across the globe, many of which are facing unprecedented rates of ecosystem change. Yet, historical information related to freshwater species, especially fishes, remains scattered, often in original formats, and underutilized for informing conservation and restoration activities. Here, we present a Data Descriptor called Coregonine Spawning History (CORHIST), a database designed to house diverse data related to past spawning and nursery areas for fishes in the family Salmonidae, subfamily Coregoninae (ciscoes and whitefishes), in the Laurentian Great Lakes and their tributaries. Data for 11 species of coregonines historically occurring in the Great Lakes are included in CORHIST. Over 3,400 occurrence records at the coordinate scale have been entered, over 2,200 of which are for Cisco (Coregonus artedi) and Lake Whitefish (C. clupeaformis)-two focal species for which there is either multinational conservation interest or restoration efforts underway in the Laurentian Great Lakes. CORHIST is already proving useful for several studies developing habitat suitability models and delineating spatial units for conservation or restoration planning.},
}

*Salmonidae
*Lakes
*Conservation of Natural Resources
Ecosystem
Great Lakes Region
Databases, Factual
Species Specificity
Animals

@article {pmid42364172,
year = {2026},
author = {Zhang, H and Liu, P and Chen, Y and Lv, J and Zhang, X and Zhang, J and Sun, Y and Wang, C and Wei, S and Wang, X and Gao, S and Qian, X and Jia, H and Tiedje, JM},
title = {Density-mediated freshwater plastisphere microbiomes preferentially degrade conventional rather than biodegradable microplastics.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag167},
pmid = {42364172},
issn = {1751-7370},
support = {2024ZY-JCYJ-02-25//Dryland Agriculture Shaanxi Laboratory Foundation/ ; 241111320200//Key R&D projects in Henan Province/ ; 2025SF-YBXM-523//Key R&D Program of Shaanxi Province/ ; 2024YFC3713900//National Key R&D Program of China/ ; 42107434//National Natural Science Foundation of China/ ; 42477394//National Natural Science Foundation of China/ ; },
mesh = {*Microplastics/metabolism ; Biodegradation, Environmental ; *Fresh Water/microbiology ; Polyesters/metabolism ; *Microbiota ; *Bacteria/metabolism/classification/genetics ; *Polypropylenes/metabolism ; *Biodegradable Plastics/metabolism ; Biofilms/growth & development ; Multiomics ; },
abstract = {The escalating demand for plastics leads to ubiquitous microplastic (MP) pollution worldwide. Existing evidence suggests that biodegradable MPs degrade faster than conventional MPs in aquatic environments. Here, we demonstrate the greater biodegradability of conventional polypropylene (PP) over biodegradable polylactic acid (PLA) in freshwater based on field survey, mesocosm experiment, co-culture assay, and multi-omics analysis. The biodegradation rate is 3.3-fold higher for PP compared to PLA, and this difference is more pronounced between photoaged MPs (5.7-fold). The unexpected superior biodegradability of PP is supported by a greater diversity of MP-degrading bacteria in PP biofilm (predominantly aerobes) than in PLA biofilm (mainly facultative and obligate anaerobes). The inferior biodegradability of PLA is attributed to microbial growth constraints in the plastisphere driven by oxic-to-hypoxic/anoxic transition, oxygen-containing functional group detachment from the polymer, and lactide accumulation during long-term biodegradation. Our findings reveal previously overlooked but important environmental fates and impacts of biodegradable plastics against increasing substitution of conventional plastics with biodegradable alternatives.},
}

*Microplastics/metabolism
Biodegradation, Environmental
*Fresh Water/microbiology
Polyesters/metabolism
*Microbiota
*Bacteria/metabolism/classification/genetics
*Polypropylenes/metabolism
*Biodegradable Plastics/metabolism
Biofilms/growth & development
Multiomics

@article {pmid42458931,
year = {2026},
author = {Vinay, KL and Goyal, N and Warudkar, A and Arvind, C and Robin, VV},
title = {Genome Assemblies for Seven Families of Birds From the Global South.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70162},
pmid = {42458931},
issn = {1755-0998},
support = {//Rohini Nilekani Philanthropies Foundation/ ; //Indian Institute of Science Education and Research Tirupati/ ; },
mesh = {Animals ; *Birds/genetics/classification ; *Genome ; India ; Sequence Analysis, DNA ; Computational Biology/methods ; Genomics/methods ; },
abstract = {Tropical regions are biodiversity-rich, yet remain underrepresented in the availability of genomic resources, as is evident in the Western Ghats of India, a biodiversity hotspot with high endemism. Here, we present high-quality, de novo genome assemblies for seven birds, representing seven families distributed in the Western Ghats: Black-naped Monarch (Monarchidae: Hypothymis azurea), Indian Yellow Tit (Paridae: Machlolophus aplonotus), Brown-cheeked Fulvetta (Leiothrichidae: Alcippe poioicephala), Malabar Trogon (Trogonidae: Harpactes fasciatus), Blue-bearded Bee-eater (Meropidae: Nyctyornis athertoni), Malabar Whistling-Thrush (Muscicapidae: Myophonus horsfieldii), Orange-headed Thrush (Turdidae: Geokichla citrina). Using a hybrid Oxford Nanopore long reads-Illumina short reads approach, we assembled genomes with sizes ranging from 1.03 to 1.13 Gbp. All assemblies demonstrated high contiguity and completeness (BUSCO scores > 97%, UCEs > 4799). Repeat masking identified ~10% of the genomes as interspersed repeats. Of the predicted protein-coding genes, an average of 9619 per species received high-confidence functional annotation hits. Comparative analysis showed our assemblies had significantly higher contiguity than the median of existing avian genomes on NCBI (Wilcoxon test, p = 0.00226). Our genome assemblies fill a key geographic and taxonomic gap in the genomic data and provide a foundational resource for evolutionary and ecological research in the Old-World tropics.},
}

Animals
*Birds/genetics/classification
*Genome
India
Sequence Analysis, DNA
Computational Biology/methods
Genomics/methods

@article {pmid42459996,
year = {2026},
author = {Filippova, N and Bulyonkova, TM and Zvyagina, E and Ageev, D and Rudykina, E and Mingalimova, A},
title = {Cortinarius barcoding database of Western Siberia and adjacent areas.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e196734},
pmid = {42459996},
issn = {1314-2828},
abstract = {BACKGROUND: The genus Cortinarius (Pers.) Grays. is a highly diverse and ecologically crucial group of ectomycorrhizal fungi in boreal forests. Despite a long history of mycological study in Russia, a comprehensive, molecularly validated inventory of its diversity in Western Siberia has been lacking. Global genetic resources are essential for modern fungal research, yet such a curated, regional dataset for this complex genus has not been previously available for this region.

NEW INFORMATION: This paper describes a curated database of 624 Cortinarius specimens from Western Siberia and adjacent regions, resulting in 624 high-quality ITS sequences. The dataset includes detailed collection metadata, morphological descriptions and photographic documentation, all standardised and linked to DNA sequence data originally managed in Specify 7. The sequences were processed through a rigorous bioinformatics pipeline with strict quality controls and assigned provisional taxonomy using a defined BLAST protocol against international reference databases. The complete dataset, including raw sequences, specimen data and collection images, has been deposited in international repositories (Global Biodiversity Information Facility (GBIF) (https://doi.org/10.15468/4v8km8), Sequence Reads Archive (SRA) and GenBank), providing a foundational resource for future taxonomic, phylogenetic and ecological studies on this key fungal genus in Western Siberia.},
}

@article {pmid42460566,
year = {2026},
author = {Mortazavi, S and Alazaiza, MYD and Nikolova, MP and Naeijian, F and Choi, H and Sillanpää, M},
title = {Review on magnetic chitosan nanomaterials as sustainable adsorbents for water pollution control.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {94},
number = {1},
pages = {198-214},
pmid = {42460566},
issn = {0273-1223},
support = {BG16RFPR002-1.014-0004//Centre of Excellence "Universities for Science, Informatics and Technologies in e-Society" (UNITe), funded by the Ministry of Innovation and Growth of the Republic of Bulgaria under the Program "Research, Innovation and Digitalization for Smart Transformation" (PRIDST) and co-funded by the European Union through the ERDF/ ; },
mesh = {*Chitosan/chemistry ; Adsorption ; *Water Purification/methods ; Water Pollutants, Chemical/chemistry ; *Water Pollution/prevention & control ; *Nanostructures/chemistry ; Magnetics ; },
abstract = {Adsorption stands out for its simplicity, cost-effectiveness, and high efficiency in removing a wide range of contaminants. However, traditional adsorbents often suffer from limited capacity, selectivity, and reusability. In response to these limitations, a significant research effort has recently focused on developing magnetic chitosan nanomaterials (MCNMs), which combine the inherent biodegradability and biocompatibility of chitosan with magnetic responsiveness for easy separation and reusability. Previous articles reviewed general MCNMs, primarily focusing on their adsorption mechanisms and performance in removing specific pollutants. This review comprehensively discusses recent advances in nanoscale modification of the materials and their applications for enhanced treatment of water containing various heavy metals and pharmaceuticals. A detailed comparison is provided between conventional chitosan materials and their magnetic nano-engineered counterparts (MCNMs), emphasizing improvements in adsorption capacity, kinetics, and regeneration potential. This review also highlights key factors that govern adsorption efficacy, such as pH, surface modification, and pollutant type. By reviewing current trends and challenges in the field, this work aims to guide future research toward the design of more efficient and sustainable water treatment systems, offering a forward-looking perspective on the potential of MCNMs for real-world water and wastewater treatment applications.},
}

*Chitosan/chemistry
Adsorption
*Water Purification/methods
Water Pollutants, Chemical/chemistry
*Water Pollution/prevention & control
*Nanostructures/chemistry
Magnetics

@article {pmid42429454,
year = {2026},
author = {Di Leo, D and Nilsson, E and Westmeijer, G and Pinhassi, J and Lundin, D},
title = {nf-core/magmap: Map metatranscriptomes to large collections of genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/bioinformatics/btag501},
pmid = {42429454},
issn = {1367-4811},
support = {//Linnaeus University/ ; 2019-00242//Swedish Research Council VR Swedish Biodiversity Data Infrastructure (SBDI)/ ; 2023-00184//Swedish Research Council VR Swedish Biodiversity Data Infrastructure (SBDI)/ ; 2023-03401//Swedish Research Council VR/ ; //Swedish strong research environment EcoChange/ ; 23-0228//Kempe Foundation/ ; //National Academic Infrastructure for Supercomputing in Sweden (NAISS)/ ; 2025/22-936//NAISS/ ; 2025/6-241, NAISS 2025/22-489//NAISS/ ; 2025/23-189//NAISS/ ; 2022-06725//Swedish Research Council/ ; },
mesh = {*Software ; *Metagenomics/methods ; *Chromosome Mapping/methods ; *Genome ; Databases, Genetic ; *Metagenome ; },
abstract = {SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes.

The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).},
}

*Software
*Metagenomics/methods
*Chromosome Mapping/methods
*Genome
Databases, Genetic
*Metagenome

@article {pmid42424959,
year = {2026},
author = {Khan, S and Zeb, A and Ullah, K and Shi, R and Zhao, Y and Tariq, H and Baig, AM and Li, X and Iqbal, H and Hussain, S and Wu, Z and Liu, W},
title = {Unraveling jasmonic acid-mediated mitigation of 6PPD toxicity in tomato plants using multi-omics approaches.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142926},
doi = {10.1016/j.jhazmat.2026.142926},
pmid = {42424959},
issn = {1873-3336},
mesh = {*Cyclopentanes/pharmacology ; *Oxylipins/pharmacology ; *Solanum lycopersicum/drug effects/metabolism/genetics/growth & development ; Multiomics ; Metabolomics ; Molecular Docking Simulation ; Oxidative Stress/drug effects ; *Plant Growth Regulators/pharmacology ; Photosynthesis/drug effects ; },
abstract = {The widespread application of the tire antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) has driven the pervasive environmental occurrence of its toxic quinone transformation product, 6PPD-quinone, raising significant ecological concerns and necessitating effective mitigation strategies. However, despite the widespread use of external biomass-based remediation strategies for environmental cleanup, internal physiological mitigation approaches to alleviate 6PPD induced phytotoxicity in plants are still lacking. Herein, we establish a multi-level phytoprotection framework, investigating the protective role of foliar-applied jasmonic acid (JA) against 6PPD toxicity in tomato plants through the integration of physiological assessments, multi omics (transcriptomics and metabolomics) analyses and molecular docking simulation. Physiological results revealed that 6PPD exposure triggered severe oxidative stress, inhibiting plant growth and impairing photosynthetic functions. Exogenous JA application effectively mitigated these adverse effects and restored physiological homeostasis. Integrated omics analyses revealed that JA mediated a comprehensive reprogramming of the plant's metabolic and transcriptional landscape to counteract 6PPD toxicity. Specifically, JA redirected metabolic flux by enhancing carbohydrate metabolism to fuel defense responses, while transcriptionally reallocating resources from growth-related processes toward the activation of specialized metabolic pathways, particularly flavonoid biosynthesis. Molecular docking further demonstrated that JA possessed a high binding affinity for key enzymes (e.g., chalcone synthase) in the flavonoid biosynthesis pathway, providing a mechanistic basis for its regulatory role. These findings highlight a promising internal defense strategy, warranting further validation under field conditions and across a broader range of crops and organic contaminants.},
}

*Cyclopentanes/pharmacology
*Oxylipins/pharmacology
*Solanum lycopersicum/drug effects/metabolism/genetics/growth & development
Multiomics
Metabolomics
Molecular Docking Simulation
Oxidative Stress/drug effects
*Plant Growth Regulators/pharmacology
Photosynthesis/drug effects

@article {pmid42452269,
year = {2026},
author = {Pieroni, A and Alrhmoun, M and Ullah, I and Hajdari, A and Bajrami, A and Kalle, R and Sulaiman, N and Sõukand, R},
title = {Continuity and Change in the Arbëreshë Wild Food Plant Foraging in Inland Southern Italy.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
pmid = {42452269},
issn = {2223-7747},
abstract = {This study investigates the ethnobiology of wild food plants in Arbëreshë (Albanian-speaking) and neighbouring Calabrian communities in north-eastern Calabria, inland southern Italy. It examines how traditional ecological knowledge, plant use patterns, and cultural perceptions are represented across two datasets, contributing to the understanding of biocultural dynamics in Mediterranean rural contexts. Fieldwork was conducted through forty-six semi-structured interviews in five villages in north-eastern Calabria, Southern Italy. Data were compared with an ethnobotanical dataset collected in the Vulture area (northern Lucania, southern Italy) during 2000-2001. The comparison is treated as cross-spatial and diachronic at the level of observed ethnobotanical records. Because the study areas differ in ecological and socio-economic conditions, comparisons are presented as descriptive contrasts rather than as direct temporal change. Taxa were classified by citation frequency, and comparisons were conducted at genus level to describe patterns of presence and variation in reported wild plant use. A total of 82 wild food taxa were documented. The dataset was dominated by vascular plants, with frequent representation of the families Asteraceae, Brassicaceae, Apiaceae, and Lamiaceae. Arbëreshë participants reported 60 genera, including seven genera not recorded in the comparative dataset (Asphodeline, Pimpinella, Hirschfeldia, Silene, Bellevalia, Leontodon, and Crocus). Calabrian participants reported 28 genera, including three not recorded among Arbëreshë participants (Clinopodium, Suillus, and Urospermum). Twenty-one genera were present in both datasets. Differences in citation frequency and genus composition are observed between datasets, with variation across groups and contexts. The results show a shared set of commonly reported wild food taxa across datasets, alongside variation in less frequently reported genera. The findings describe differences in ethnobotanical records across communities and time-separated datasets, reflecting combined influences of ecological context, sampling conditions, and local knowledge practices.},
}

@article {pmid42455829,
year = {2026},
author = {Calahorro, F and Fouladi, P and Pandini, A and Khushi, M and Gaihre, Y and Bury, NR},
title = {Binding Affinity Ranking at the Molecular Initiating Event (BARMIE): An open-source computational pipeline for the rapid screening of chemical interactions with steroid receptors from many species.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353622},
pmid = {42455829},
issn = {1932-6203},
mesh = {Animals ; *Receptors, Glucocorticoid/metabolism/chemistry ; Protein Binding ; Ligands ; *Receptors, Steroid/metabolism/chemistry ; Hydrocortisone/metabolism/chemistry ; Oncorhynchus mykiss/metabolism ; Binding Sites ; Glucocorticoids/metabolism/chemistry ; *Computational Biology/methods ; Computer Simulation ; Fishes/metabolism ; },
abstract = {A challenge in ecological risk assessment is identifying the chemicals that pose the greatest threat and determining which species are most vulnerable to them. To help address this, this study has developed an in-silico open-source tool called BARMIE (Binding Affinity Ranking at the Molecular Initiating Event) to rapidly predict the chemical binding affinity of steroid receptor proteins to synthetic steroids to identify potentially vulnerable species and chemicals of concern. BARMIE was used to screen 163 teleost fish glucocorticoid receptors (GRs) for binding to the natural ligand cortisol and to 10 synthetic glucocorticoid drugs (GCs) designed to interact within the ligand-binding pocket (LBP) of GRs. BARMIE identified species from the superorder Protacanthopterygii with high-affinity GRs to synthetic GCs (e.g., vulnerable species).. BARMIE was also used to screen binding profiles of compounds in the Medicine for Malaria Venture Global Health Priority Box to rainbow trout GRs (rtGR1 and rtGR2). Of the 178 compounds, 24 and 36 bind within the LBP of rtGR1 and rtGR2, respectively. For 30 of these compounds, transactivation activity was assessed at 1µM in the presence or absence of 1µM cortisol and confirmed 2 compounds with agonistic properties (e.g., chemicals of concern) that would require further in vitro and/or in vivo studies to assess the environmental risk. BARMIE can rapidly generate predicted binding affinities for 100's of species and chemicals as a first screen in environmental risk assessment to provide information on which substances to prioritise in downstream tests.},
}

Animals
*Receptors, Glucocorticoid/metabolism/chemistry
Protein Binding
Ligands
*Receptors, Steroid/metabolism/chemistry
Hydrocortisone/metabolism/chemistry
Oncorhynchus mykiss/metabolism
Binding Sites
Glucocorticoids/metabolism/chemistry
*Computational Biology/methods
Computer Simulation
Fishes/metabolism

@article {pmid42457409,
year = {2026},
author = {Liang, LW and Fatimah, A and Qian, Q and Zhang, T and Wang, XY and Zhang, FY and Xiao, Q and Guo, ZG and Jiang, AL and Zhao, XY and Wu, XG and Du, MX and Yu, JY and Liu, HC and Chen, YH and Jiang, JP and Liao, ZY},
title = {Global Camera Trapping Inventory (GCTI) v.1.0: A worldwide inventory of camera-trapping studies for spatial biodiversity analysis.},
journal = {Zoological research},
volume = {47},
number = {4},
pages = {1097-1105},
doi = {10.24272/j.issn.2095-8137.2025.340},
pmid = {42457409},
issn = {2095-8137},
mesh = {*Biodiversity ; Animals ; *Photography ; Conservation of Natural Resources/methods ; *Databases, Factual ; },
abstract = {Camera traps have significantly advanced biodiversity monitoring by enabling standardized, noninvasive detection of medium- and large-sized wildlife across broad spatial scales. However, the lack of data sharing within the camera-trapping community, particularly during the early development of the field, has restricted the availability of public species-occurrence records and limited the integration of camera-trap evidence into global spatial analyses. Data sensitivity, especially for threatened species, has further constrained open access to study-level geographic records. To address this gap, the Global Camera Trapping Inventory (GCTI) v.1.0 was developed to compile project-level spatial information from 970 camera-trapping studies indexed in the Web of Science (WoS) and China National Knowledge Infrastructure (CNKI) between 1990 and 2023. The database includes an Excel file with 22 fields documenting study design, survey methods, recorded taxa, and associated metadata, together with three shapefile formats that capture geographic information at complementary spatial resolutions. The GCTI database was established to strengthen open, collaborative data sharing in biodiversity monitoring while preserving the spatial structure needed for research synthesis. By providing project-level shapefiles linked to specific regions and species, GCTI offers a spatially explicit resource for biodiversity, conservation, ecology, and biogeography research. Compared with existing platforms such as Wildlife Insights and eMammal, GCTI provides data suitable for meta-analyses, literature reviews, and spatial overlap analyses with global biodiversity resources, such as GBIF and the IUCN Red List. To facilitate data access and application, an interactive web platform was developed to enable online searching, visualization, and download (https://biodiversityoptimization.shinyapps.io/gcti_v1/).},
}

*Biodiversity
Animals
*Photography
Conservation of Natural Resources/methods
*Databases, Factual

@article {pmid42151184,
year = {2026},
author = {Ma, F and Huang, H and Yang, Q and Altermatt, F and Hong, P and Luo, M and Wang, S},
title = {Biodiversity and habitat complexity buffer the destabilizing effects of anthropogenic activities on riverine fish communities.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42151184},
issn = {2041-1723},
support = {32588202//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32425036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32301349//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Humans ; *Anthropogenic Effects ; *Biodiversity ; Datasets as Topic ; *Fishes ; Latent Class Analysis ; Population Dynamics ; *Rivers ; Spatial Analysis ; Temperature ; Conservation of Natural Resources ; },
abstract = {Riverine fish communities are essential for the functioning of aquatic ecosystems and provide important ecosystem services for fisheries. Yet, anthropogenic environmental changes pose threats to fish communities and result in population collapses and reduced yields, underscoring the need to understand their stability from local to regional scales. In this study, we leverage long-term observational data of riverine fish communities in 108 hydrological basins across the globe to determine how anthropogenic activity, biodiversity, and habitat complexity jointly influence riverine fish community stability (i.e., temporal invariability of total fish abundance) at the site and basin scales. Our analyses show that anthropogenic activities represented by human footprint index decrease fish community stability across spatial scales; however, biodiversity and habitat complexity buffer these destabilizing effects by providing insurance effects at both site and basin scales. Specifically, biodiversity has consistently stabilizing effects across scales through enhancing the asynchrony within and/or among fish communities. At the basin scale, greater habitat area increases gamma stability by enhancing spatial community asynchrony. Our findings underscore the importance of conserving both fish biodiversity and habitat complexity to sustain the stability of riverine fish communities in the Anthropocene.},
}

Animals
Humans
*Anthropogenic Effects
*Biodiversity
Datasets as Topic
*Fishes
Latent Class Analysis
Population Dynamics
*Rivers
Spatial Analysis
Temperature
Conservation of Natural Resources

@article {pmid42364396,
year = {2026},
author = {Wang, LM and Montanari, A and Gal, N and Chaix, B and Birenboim, A},
title = {Temporal patterns of smartphone-mediated digital engagement and mental health symptomatology.},
journal = {Acta psychologica},
volume = {268},
number = {},
pages = {107259},
doi = {10.1016/j.actpsy.2026.107259},
pmid = {42364396},
issn = {1873-6297},
mesh = {Humans ; *Smartphone/statistics & numerical data ; Female ; Male ; *Anxiety/psychology ; Adult ; *Depression/psychology ; Ecological Momentary Assessment ; Digital Media ; Young Adult ; Middle Aged ; Media Exposure ; Time Factors ; Digital Health ; Mental Health ; },
abstract = {Current ubiquitous information and communication technologies are reshaping human behaviours and could have profound implications for mental health. To investigate the dynamic patterns of daily interactions with the digital environment-particularly via smartphones-a novel, ecological approach is implemented which incorporates the use of innovative sensors. Data was collected from 31 healthy individuals from the general population living in Jerusalem who were tracked using objective smartphone logs of digital activity and daily self-reports of anxiety and depression symptoms. Significant associations were found between temporal patterns of smartphone usage and momentary anxiety symptomatology. Higher levels of overall phone usage in the morning hours were a significant predictor of anxiety while high levels of phone usage in the rest of the day were associated with decreased anxiety symptoms. A more nuanced analysis of usage types revealed that high levels of social and process-related digital activity in the morning were associated with a reduction in anxiety symptoms, with evidence of a dose-response relationship. These findings highlight the importance of context, user motivation, and the complex relationship between smartphone usage and mental health which warrant further research.},
}

Humans
*Smartphone/statistics & numerical data
Female
Male
*Anxiety/psychology
Adult
*Depression/psychology
Ecological Momentary Assessment
Digital Media
Young Adult
Middle Aged
Media Exposure
Time Factors
Digital Health
Mental Health

@article {pmid42449219,
year = {2026},
author = {Qu, S and Xu-Ri, and Yu, J and Shama, R and Lei, H and Tian-Liang, and Bayarsaikhan, S and Jukov, A and Tsendeekhuu, M and Vanjil, G and Borjigidai, A},
title = {Climatic controls on water-use efficiency and nitrogen acquisition of Astragalus on southwestern Tibetan Plateau.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09356-2},
pmid = {42449219},
issn = {1471-2229},
support = {U21A20185//National Natural Science Foundation of China/ ; 2019QZKK0606//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2022YFE0119300//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The southwestern Tibetan Plateau (TP) is characterized by cold and dry alpine grasslands, yet how plants and soil nitrogen cycles adapt to conditions that are drier and colder than other parts of the TP remain unclear. We measured δ[13]C and δ[15]N in Astragalus, a widespread N-fixing legume, and soils along a 3500-5000 m transect in the southwestern TP.

RESULTS: Plant δ[13]C and inferred intrinsic water-use efficiency (iWUE, 85.6-114.2 μmol CO2 mol[-1] H2O) were primarily controlled by growing-season temperature (GST), with SEM showing a significant direct effect of GST on iWUE (standardized path coefficient = 0.45, p < 0.01). Conversely, soil δ[15]N (2.8‰ to 11.3‰) was negatively associated with mean annual precipitation (MAP; R[2] = 0.26, p < 0.01), while plant-soil Δ[15]N was mainly driven by mean annual precipitation (MAP, R[2] = 0.24, p < 0.01). These Δ[15]N patterns may reflect shifts in the relative contribution of atmospheric N2 fixation and soil N uptake by Astragalus, as inferred from isotopic evidence.

CONCLUSIONS: These results suggest potential responses of plant carbon-water coupling and isotope-inferred N acquisition under future warming and drying in high-elevation ecosystems.},
}

@article {pmid42451887,
year = {2026},
author = {Matyjas-Zgondek, E and Kulpiński, P and Skiba, E and Popczyk, M and Swinarew, AS},
title = {Long-Lasting Photocatalytic and Antimicrobial Activity of Cotton Dishcloths Finished with TiO2 Nanoparticles and Zinc Pyrithione.},
journal = {Materials (Basel, Switzerland)},
volume = {19},
number = {13},
pages = {},
pmid = {42451887},
issn = {1996-1944},
abstract = {This study assesses the durability of self-cleaning and antimicrobial activities of dishcloths made of 100% cotton woven fabric modified with TiO2 nanoparticles (NPs) and zinc pyrithione particles (ZnPt). The self-cleaning properties were measured as the ability to decompose staining particles via photocatalytic action under UV/VIS light irradiation and confirmed by colour measurements (K/S values, colour differences, and colour changes ΔL*, Δa*, Δb*). The SEM micrographs confirmed the long-term durability of the modification process, and ICP-OES analysis confirmed the presence of Ti and Zn elements on and within the fabric. The amounts of TiO2 and ZnPt decreased by 2.2-2.5 times after the first 5 washings and by 2.1-1.2 times after the subsequent 45 washings. Antimicrobial activity was tested against Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 11229 and Candida albicans ATCC 10231. The results indicate that the material maintains excellent self-cleaning properties and good antimicrobial activity for up to 50 washings; however, activity against E. coli remains weak after 30 and 50 washings.},
}

@article {pmid41678595,
year = {2026},
author = {Davis, KP and Eaton, MJ and Bjerre, ER and White, HM and Boal, CW and Herner-Thogmartin, JH and Robinson, OJ and Lawson, AJ},
title = {Constructed value of information with iterative scoring and parametric uncertainty to identify management-relevant research priorities for a declining raptor species.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {40},
number = {4},
pages = {e70227},
pmid = {41678595},
issn = {1523-1739},
support = {G22AC00121//U.S. Geological Survey/U.S. Fish and Wildlife Service Science Support Partnership Program/ ; },
mesh = {Animals ; *Conservation of Natural Resources/methods ; Uncertainty ; *Falconiformes/physiology ; *Decision Support Techniques ; Population Dynamics ; },
abstract = {Constructed value of information (CVoI) is an expert elicitation decision-analytic tool used to prioritize sources of uncertainty based on their potential to improve decision outcomes if resolved. Despite increased application of CVoI, the robustness of CVoI prioritization of sources of uncertainty relative to differences in expert elicitation and scoring methods has not been evaluated. We engaged a group of species experts in a decision-analytic process to elicit uncertainties, framed as alternative hypotheses, about current population declines of the American kestrel (Falco sparverius) in the United States. Participants scored 13 hypotheses across 3 CVoI criteria, which are defined as constructed scales. Rather than experts selecting a single score per criterion, we used a likelihood point method to incorporate parametric uncertainty in the scoring process, in which experts were given 100 points to distribute across possible score categories within the criterion-specific constructed scale. Experts provided scores over 2 scoring rounds, with an opportunity to review and discuss initial scores between rounds. We used a Shannon entropy calculation to quantify how evenly participants allotted their points. We used simulation to evaluate the robustness of our prioritization results relative to a scoring method in which participants selected a single score category for each criterion. Participants often spread their points across 2 adjacent scores, reflecting parametric uncertainty. For one third of the hypothesis-scoring round combinations, the prioritization results differed in approximately 50% of simulations. The highest scoring hypotheses related to how the use of artificial versus natural nest cavities affects fecundity or survival, whether winter roosting sites are a limiting factor for population growth, and whether gamebird habitat management may benefit kestrel populations. Our CVoI prioritization framework can be used to develop collaborative research that is directly relevant to a management decision and is an advance in eliciting more representative expert beliefs.},
}

Animals
*Conservation of Natural Resources/methods
Uncertainty
*Falconiformes/physiology
*Decision Support Techniques
Population Dynamics

@article {pmid41814567,
year = {2026},
author = {Pelage, L and Brunel, A and Fache, E and Frédou, T and Lanco, S and Lucena-Frédou, F and Bertrand, A},
title = {Guiding stakeholder negotiations in data-poor coastal planning with open-access spatial data.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {40},
number = {4},
pages = {e70248},
pmid = {41814567},
issn = {1523-1739},
support = {734271//Horizon 2020/ ; },
mesh = {*Conservation of Natural Resources/methods ; Brazil ; Fisheries ; *Negotiating ; *Ecosystem ; Tourism ; Decision Support Techniques ; Satellite Imagery ; },
abstract = {Negotiating conservation priorities in highly anthropic ecosystems requires approaches that promote cooperation and cost bargaining among stakeholders. In data-poor contexts, such negotiations are hindered by limited information and conflicting interests. We developed a transparent and reproducible prioritization framework, combining open-access satellite imagery with a decision-support tool, to inform participatory coastal planning. Although illustrated in northeast Brazil, a data-poor region where coastal conflicts between tourism and fisheries are acute, the framework was designed to be broadly applicable to similar coastal social-ecological systems. It generates visualizations that help stakeholders explore trade-offs in three dimensions: defining a conservation target; debating the location of coastal candidate areas that balance habitat protection with minimizing impacts on tourism and fishing activities; and deliberating the degree of restriction within each candidate area based on conservation and socioeconomic considerations. We applied this approach to design five alternative spatial planning scenarios. Three were based on composite tourism and fisheries indices ("neutral", "avoid fisheries areas", and "avoid tourism areas"), and two focused on specific practices ("all specific activities" and "do not exclude small-scale"). These scenarios revealed where restrictions can be applied or relaxed to achieve conservation objectives while maintaining essential local livelihoods. By highlighting the limitations of existing conservation units and promoting inclusive, transparent decision-making, our method provides a practical means to focus stakeholder negotiations. More broadly, the framework offers a scalable and transferable approach for equitable, multisectoral conservation planning in other data-poor coastal regions facing similar trade-offs.},
}

*Conservation of Natural Resources/methods
Brazil
Fisheries
*Negotiating
*Ecosystem
Tourism
Decision Support Techniques
Satellite Imagery

@article {pmid42349033,
year = {2026},
author = {Cárdenas-Conejo, Y},
title = {GenomoBase: A comprehensive resource for the family Genomoviridae.},
journal = {Virology},
volume = {623},
number = {},
pages = {111018},
doi = {10.1016/j.virol.2026.111018},
pmid = {42349033},
issn = {1096-0341},
mesh = {*DNA Viruses/genetics/classification/isolation & purification ; *Genome, Viral ; Metagenomics ; Animals ; Metagenome ; *Databases, Genetic ; Phylogeny ; },
abstract = {The family Genomoviridae comprises circular single-stranded DNA viruses reported from fungi, plants, animals and environmental samples. Although metagenomics has accelerated their discovery, genomic sequences, annotations and metadata remain dispersed across repositories. Here we present GenomoBase (https://www.genomobase.org), a curated resource that integrates genomic, ecological and bibliographic data for all 237 ICTV-recognized genomovirus species. GenomoBase incorporates Serratus-filtered SRA screening outputs, enabling prioritization of metagenomes for targeted re-analysis. As a proof of concept, a targeted bait-and-assemble workflow of one prioritized SRA run reconstructed two candidate complete circular genomovirus genomes from metagenomic reads, both below the 78% species demarcation threshold for genomoviruses. Overall, GenomoBase supports comparative analyses and taxonomically informed exploration of public metagenomes.},
}

*DNA Viruses/genetics/classification/isolation & purification
*Genome, Viral
Metagenomics
Animals
Metagenome
*Databases, Genetic
Phylogeny

@article {pmid42442356,
year = {2026},
author = {Nguyen, TN and Cosgrove, EJ and Chen, N and Lehr, N and Lokey, MG and Beaudry, FEG and Fitzpatrick, SW and Bowman, R and Miller, KE and Fitzpatrick, JW and Clark, AG},
title = {Florida scrub-jay genomes across space and time reveal impacts of population decline and reduced gene flow.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2026.06.044},
pmid = {42442356},
issn = {1879-0445},
abstract = {Whole-genome sequencing is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) was more numerous across peninsular Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, a reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay.},
}

@article {pmid42443342,
year = {2026},
author = {Zhuang, Y and He, G and Xi, W and Zhang, J and Wang, R and Jin, T and Zhu, Y and Fu, J},
title = {Environmental space similarity model maps dry red soil under limited samples in the Yuanmou Dry Hot Valley.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61912-w},
pmid = {42443342},
issn = {2045-2322},
support = {202304BT090025-04//Yunnan Provincial Science and Technology Department, Yunnan Innovation Guidance and Cultivation Program for Science and Technology Enterprises - "Building Yuanmou County as a Science and Technology Innovation County for Rural Revitalization" Project/ ; 202205AK070026-01//Yunnan Key Laboratory of Soil Erosion Prevention and Green Development/ ; 202202AD080010//Major scientific and technological projects of Yunnan Province: Research on Key Technologies of ecological environment monitoring and intelligent management of natural resources in Yunnan/ ; KLMHER-K25//Supported by "the Open Funds of the Key Laboratory of Mountain Hazards and Engineering Resilience, Chinese Academy of Sciences"/ ; 202305AS350003//Yunnan Province Innovation Team Project/ ; },
abstract = {Obtaining sufficient field observations for natural resources in complex mountainous environments is often constrained by limited soil samples. Geographic environmental similarity may provide a useful basis for spatial inference under small-sample conditions. Here we infer the spatial distribution of dry-red soil in the Yuanmou Dry-Hot Valley, China. Field surveys produced a training set (n = 72) and an independent validation set (n = 46; dry-red soil/non-dry-red soil = 1:1). After screening covariates related to soil, terrain, climate, and vegetation, we quantified environmental similarity among samples and computed a composite similarity score. Using stratified repeated random splitting on the independent validation set, we calibrated the classification threshold, built an Environmental Similarity Model (ESM), and generated an uncertainty layer for interpretation and extrapolation-risk identification. Results show that (1) dry-red soil is mainly distributed in basins and valley areas; (2) the ESM showed relatively strong performance on the independent validation set within the present study area (mean AUC = 0.946, Accuracy = 0.867, Recall = 0.870, F1-score = 0.862), exceeding the benchmark machine-learning models under the current validation design (mean AUC = 0.654-0.809, Accuracy = 0.589-0.707); and (3) the uncertainty layer identifies environmentally under-represented areas with higher extrapolation risk, which may support prioritized supplementary sampling and iterative updating. Overall, these results suggest that the ESM provides an interpretable option for dry-red soil inference under the present small-sample and heterogeneous environmental setting.},
}

@article {pmid42443631,
year = {2026},
author = {Flannery, JL and Engelhard, MM and Kansagra, S and Kollins, SH and Krystal, A and Lunsford-Avery, JR},
title = {Leveraging convenient wearable technology to assess adolescent sleep: physical and behavioral health correlates of single-channel sleep electroencephalogram in a community sample of youth.},
journal = {Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine},
volume = {22},
number = {1},
pages = {},
pmid = {42443631},
issn = {1550-9397},
support = {5T32-MH132515-02//National Institute of Health Sciences/ ; },
mesh = {Humans ; Female ; Adolescent ; Male ; *Electroencephalography/instrumentation/methods ; *Wearable Electronic Devices ; Child ; *Sleep Wake Disorders/diagnosis/physiopathology ; Sleep Duration ; Digital Health ; },
abstract = {STUDY OBJECTIVES: Sleep disturbances during adolescence heighten risk for physical and behavioral health problems, yet sleep physiological markers critical to health outcomes are rarely assessed in pediatric care. Wearable single-channel electroencephalography (EEG) devices may offer scalable, ecologically valid methods for assessing sleep physiology in home settings. This study evaluated whether single-channel sleep-EEG metrics were associated with physical and behavioral health in adolescents.

METHODS: Eighty-five community-derived adolescents (ages 11-17, 50% female) completed seven consecutive nights of at-home, single-channel sleep-EEG, physical health assessments (i.e., body mass index and blood pressure), and subjective sleep and behavioral health measures. Parents provided psychiatric diagnosis history.

RESULTS: Odds of being overweight/obese decreased with greater REM duration (- 2.72% per minute) and higher REM percentage (- 100% per 1%). Odds of hypertension decreased with greater time spent in stage 3 (N3) (- 4.78% per minute). Multivariate analyses showed reduced N3 sleep was associated with parent-reported ADHD symptoms, whereas shorter total sleep time, lower sleep efficiency (SE), and longer sleep onset latency (SOL) were associated with higher adolescent-reported ADHD and conduct problems (p's < .05). Odds of an ADHD diagnosis increased with longer SOL (+ 1.92% per minute) and slower N3 decline (+ 89.4% per 0.01 units) but decreased with higher SE (- 7.78% per 1%). Odds of an internalizing disorder increased with higher SE (+ 12.4% per 1%) and greater wake after sleep onset (+ 3.18% per minute), but decreased with more REM sleep (- 9.62% per minute).

CONCLUSIONS: Findings highlight the clinical value of wearable sleep-EEG for detecting sleep-related risk processes during adolescence. By capturing physiological features not accessible through self-report, at-home sleep-EEG may flag youth who could benefit from sleep-focused interventions, complementing routine care in identifying risk of future health problems. Integrating such tools into pediatric settings could support more precise, developmentally informed approaches to prevention and intervention.

CURRENT STUDY/STUDY RATIONALE: Sleep disturbances are common during adolescence and increase risk for physical conditions such as obesity and hypertension, as well as behavioral health problems, yet sleep physiology is rarely adequately assessed in pediatric care. Wearable single-channel EEG offers an accessible way to capture sleep architecture and continuity that subjective reports cannot provide. This study shows that EEG-derived sleep features, including REM, N3 sleep, sleep efficiency, and sleep-onset latency, are associated with physical and behavioral health outcomes above and beyond adolescent and caregiver reports.

STUDY IMPACT: These findings highlight the potential value of integrating wearable EEG into routine care to identify sleep-related vulnerabilities and support targeted prevention efforts.},
}

Humans
Female
Adolescent
Male
*Electroencephalography/instrumentation/methods
*Wearable Electronic Devices
Child
*Sleep Wake Disorders/diagnosis/physiopathology
Sleep Duration
Digital Health

@article {pmid42445293,
year = {2026},
author = {Jo, TS and Murakami, H},
title = {Variability in Fish Environmental DNA Concentration in Coastal Ecosystems at Hierarchical Levels: Focusing on the Magnitude, Structure, and Environmental Dependence.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74002},
pmid = {42445293},
issn = {2045-7758},
abstract = {Understanding variability in environmental DNA (eDNA) concentration is essential for improving the precision of quantitative eDNA analyses. While previous laboratory and field studies suggest that technical variation arising from sampling and PCR processes is relatively small, the hierarchical structure of this variability and its environmental dependence remain poorly understood. In this study, we conducted spatiotemporally replicated seawater sampling from a coastal ecosystem, quantified Japanese jack mackerel (Trachurus japonicus) eDNA concentrations using quantitative real-time PCR (qPCR), and assessed the magnitude, structure, and environmental drivers of eDNA variability across multiple levels. Variance component analysis revealed that more than 90% of the total variance in eDNA concentration was explained by differences among sampling sites and time points, reflecting differences in organismal distribution and dynamics, whereas sampling and PCR steps together contributed less than 10%. Using Taylor's Power Law, we demonstrated that the relationship between mean eDNA concentration and variance differed across hierarchical levels, with stronger mean-variance scaling at larger spatial and temporal scales. Notably, the relative contribution of the PCR level to the total variance increased substantially under low-concentration conditions, indicating that stochastic measurement error becomes dominant when eDNA is scarce. We also demonstrated that the PCR-level variability (Coefficient of variance; CV) increased with chlorophyll-α and decreased with pH, whereas no significant environmental effects were detected at the sample level. These results suggest that different mechanisms govern variability at each hierarchical level, including ecological processes, physical heterogeneity, and biochemical constraints. Our findings highlight that optimal sampling and replication strategies should be tailored to expected eDNA concentrations and environmental conditions in the field, helping provide a framework for maximizing signal-to-noise ratios in quantitative eDNA studies.},
}

@article {pmid41933506,
year = {2026},
author = {Qiu, CW and Zhang, S and Gao, ZF and Chen, ZH and Zhang, C and Ali, MA and Wu, F},
title = {First Tetraploa Genome and Multi-Omics Analysis Reveal Key Plant-Microbe-Soil Interactions for Salt Tolerance and Yield Improvement of Wheat.},
journal = {Plant biotechnology journal},
volume = {24},
number = {8},
pages = {4748-4765},
pmid = {41933506},
issn = {1467-7652},
support = {32161143035//National Natural Science Foundation of China/ ; BP0618021//the 111 Project of China/ ; FT210100366//Australian Research Council/ ; WSU2303-001RTX//Grains Research and Development Corporation/ ; },
mesh = {*Triticum/microbiology/growth & development/genetics/physiology/metabolism ; *Salt Tolerance/genetics ; Multiomics ; Rhizosphere ; Soil Microbiology ; *Genome, Fungal ; },
abstract = {Salinity is a major threat to global agricultural productivity of staple crops such as wheat. Although microbial-based solutions hold promise for alleviating salinity stress, practical implementation is hindered by insufficient mechanistic characterization of bioinoculants and their interactions with plants. Here, we assembled the first complete reference genome of a halotolerant strain within the genus Tetraploa-the endophytic fungus Tetraploa sp. E00680. This novel genomic resource serves as a foundation for exploring previously uncharacterised salt tolerance mechanisms in this potential fungal inoculant. Our research demonstrates that E00680 enhances wheat yield under both controlled and field saline conditions. We found that E00680 systematically modulates the plant-microbe-soil interactions by optimizing rhizosphere microbial communities, increasing nutrient bioavailability, and triggering coordinated transcriptional and metabolic reprogramming in wheat. Notably, E00680 expands tryptophan metabolism to synergistically boost auxin biosynthesis in wheat by supplying precursors and activating relevant metabolic pathways. This cross-kingdom metabolic coupling facilitates better growth and salt tolerance in wheat plants. Our findings offer multi-omics and rhizosphere-level insights that can guide the development of microbial inoculants to enhance climate-resilient and sustainable crop production.},
}

*Triticum/microbiology/growth & development/genetics/physiology/metabolism
*Salt Tolerance/genetics
Multiomics
Rhizosphere
Soil Microbiology
*Genome, Fungal

@article {pmid42178518,
year = {2026},
author = {Porfirio-Sousa, AL and Jones, RE and Brown, MW and Lahr, DJG and Tice, AK},
title = {CSI-SSU: phylogenetic contamination screening of genomic datasets, demonstrated on The Protist 10,000 Genomes (P10K) Project.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42178518},
issn = {1471-2164},
support = {GBMF13832//Gordon and Betty Moore Foundation/ ; 2100888//National Science Foundation/ ; 2019/22815-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Phylogeny ; *Genomics/methods ; *Software ; *Eukaryota/genetics/classification ; Databases, Genetic ; *DNA Contamination ; },
abstract = {BACKGROUND: Genomic data are essential for uncovering the evolutionary history, ecological roles, and diversity of life. Yet, diverse microbial eukaryotes, predominantly unicellular and traditionally referred to as protists, remain critically underrepresented in genomic repositories, limiting our ability to address fundamental questions in eukaryotic evolution. The Protist 10,000 Genomes (P10K) initiative seeks to fill this gap by generating and compiling genomic and transcriptomic data for a wide range of microbial eukaryotes. However, large-scale sequencing efforts face persistent challenges, including contamination and imprecise taxonomic identification, particularly for poorly studied taxa that require specialized taxonomic expertise. To ensure the reliability of these resources, robust and scalable approaches for taxonomic identification and contamination screening are essential.

RESULTS: We developed CSI-SSU (https://github.com/AlexTiceLab/CSI-SSU), a command-line tool for Contaminant Sequence Investigation (CSI) that uses small subunit ribosomal RNA (SSU) sequences, chimeric sequence detection, and phylogenetic placement to rapidly identify, retrieve, and classify SSU sequences from eukaryotic genomic-level assemblies. CSI-SSU incorporates a curated SSU reference dataset representing the major known eukaryotic supergroups, with sequences and taxonomic nomenclature derived from the Protist Ribosomal Reference (PR[2]) database. In addition to detecting contaminant sequences, CSI-SSU enables approximate taxonomic assignment of the target lineage in each assembly, with resolution constrained by the current diversity represented in PR[2]. To further assess potential bacterial contamination, CSI-SSU employs bacterial BUSCO searches as a proxy. We demonstrate CSI-SSU utility and performance by screening 2,960 genomic-level assemblies spanning a broad diversity of eukaryotes from P10K. CSI-SSU efficiently detected non-target eukaryotic SSU sequences, revealing cross-group contamination. Classifications also corroborated or refined the original taxonomic assignments, with resolution depending on PR[2] representation. Bacterial BUSCO searches indicated bacterial contamination. Independent SSU and COI phylogenies of Amoebozoa supported CSI-SSU classifications, highlighting its accuracy and sensitivity.

CONCLUSION: CSI-SSU provides a scalable and reproducible framework for phylogenetically informed contamination screening and taxonomic validation of genomic and transcriptomic data. Coupling phylogenetic placement with contamination detection enabled us to distinguish high-quality P10K datasets from those requiring decontamination or additional sequencing before downstream use. These findings serve as a reference for future analyses and guide further sequencing efforts to expand the taxonomic diversity of microbial eukaryotes at the genomic level. Addressing imprecise taxonomic assignments, contamination, and reproducibility in genomic-level datasets will enhance the value of these resources and facilitate studies illuminating the evolution and diversification of eukaryotic life.},
}

*Phylogeny
*Genomics/methods
*Software
*Eukaryota/genetics/classification
Databases, Genetic
*DNA Contamination

@article {pmid42185792,
year = {2026},
author = {Mirzaei, S and Tefagh, M},
title = {MOFA: microbial optimization without forced altruism.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42185792},
issn = {1471-2105},
mesh = {Algorithms ; *Methanococcus/metabolism/genetics ; Desulfovibrio vulgaris/metabolism/genetics ; *Models, Biological ; *Computational Biology/methods ; },
abstract = {BACKGROUND: Microorganisms typically exist in communities, where interactions among them define the complexity of these ecosystems. Developing in silico frameworks to investigate the behavior and functionality of these communities is therefore essential for advancing our understanding of microbial ecology. In recent years, several computational modeling frameworks based on genome-scale models have been developed for the community-level analysis of microbial systems.

RESULTS: Here, we introduce microbial optimization without forced altruism (MOFA), a bilevel optimization framework that considers both species-level and community-level fitness criteria. By imposing constraints on species biomass in the outer problem, it prevents the forced altruism observed in previous algorithms. We applied MOFA to a toy model and to community models of Desulfovibrio vulgaris and Methanococcus maripaludis, which exhibit a cross-feeding relationship that causes the community objective to override individual fitness goals by prioritizing the export of metabolites for other community members. For this microbial community, a comparison with the results of NECom, OptCom, and Joint-FBA shows that MOFA yields predictions that better match the experimental results. Additionally, for pairs with a cross-feeding relationship in which exported metabolite production associated with this mutual interaction competes with species biomass, such as D. vulgaris and M. maripaludis, NECom fails to predict the community growth rate, whereas our method succeeds.

CONCLUSIONS: MOFA effectively analyzes community growth rates without relying on forced altruism. In cases where NECom fails to predict community growth, MOFA successfully predicts these growth rates. Furthermore, MOFA enhances computational efficiency by eliminating the need for the binary variables required in the NECom algorithm.},
}

Algorithms
*Methanococcus/metabolism/genetics
Desulfovibrio vulgaris/metabolism/genetics
*Models, Biological
*Computational Biology/methods

@article {pmid42283633,
year = {2026},
author = {Gómez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL},
title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {7},
pages = {e0210625},
doi = {10.1128/aem.02106-25},
pmid = {42283633},
issn = {1098-5336},
support = {862695//PRIORITY 'Excellent science'/ ; PDI-2021-123469OB-I00//Agencia Estatal de Investigación/ ; PID2024-161463NA-I00//Agencia Estatal de Investigación/ ; },
mesh = {*Acid Phosphatase/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Fungi/enzymology/genetics/classification ; *Fungal Proteins/genetics/metabolism ; 6-Phytase/genetics ; },
abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.},
}

*Acid Phosphatase/genetics/metabolism
*Computational Biology/methods
Phylogeny
*Fungi/enzymology/genetics/classification
*Fungal Proteins/genetics/metabolism
6-Phytase/genetics

@article {pmid42434844,
year = {2026},
author = {Chen, J and Gong, J and Wang, Z and Yang, L and Yang, Y and Xu, Q and Zhang, S and Tian, X and Yan, L and Zhou, Q},
title = {Digital Affective Resilience: A Cross-Sectional Observational Study of Anxiety-Related Chinese Social Media.},
journal = {Nursing open},
volume = {13},
number = {7},
pages = {e70691},
pmid = {42434844},
issn = {2054-1058},
mesh = {Humans ; *Social Media/statistics & numerical data ; Cross-Sectional Studies ; Male ; Female ; China ; *Anxiety/psychology ; Emotions ; Adult ; *Resilience, Psychological ; Digital Media ; Phobic Disorders/psychology ; Data Mining ; Media Exposure ; },
abstract = {BACKGROUND: Anxiety disorders, including phobias, are a growing public health concern, profoundly affecting quality of life. While existing research utilizes text-based and physiological data for detection, a multimodal, ecologically valid understanding of how anxiety is expressed and regulated in natural social contexts remains limited. Social media offers a unique setting for studying spontaneous emotional disclosure and collective coping mechanisms.

METHODS: A text-mining study was conducted on 28,349 social media comments related to phobia/anxiety from three Chinese platforms (XiaoHongShu, Zhihu, and Weibo) using convenience sampling of publicly available posts up to November 1, 2025. Social media comments related to phobia discussions were collected and analysed using the Dalian University of Technology Chinese Sentiment Vocabulary Ontology lexicon-based methods. Demographic variables were analysed using Independent Samples t-test and One-way ANOVA.

RESULTS: The most frequent emotion categories were happiness (31.6%) and surprise (15.3%), followed by fear (18.4%), sadness (14.7%), anger (12.1%), and disgust (7.9%). Gender differences based on complete-case analysis (n = 12,845) showed that female users expressed significantly more happiness- and sadness-related language than male users (p = 0.005 and p = 0.034, respectively). The sentiment classifier achieved moderate performance (F1 = 0.72).

CONCLUSION: The emotional discourse surrounding phobia on Chinese social media reflects co-occurring linguistic patterns of fear alongside happiness, surprise, sadness, anger, and low-frequency disgust, rather than fear amplification alone. These findings suggest that online communication may shape how anxiety-related emotions are collectively expressed and interpreted, although causal inferences cannot be drawn from cross-sectional text data.

This study addressed the limited understanding of anxiety-related emotional expression on Chinese social media. The findings showed that anxiety discourse involved not only fear, but also supportive, empathetic, and coping-oriented emotions. These results may help nurses and mental health professionals better understand digital emotional communication, improve psychosocial support, and inform AI-assisted emotional monitoring and online mental health interventions.

REPORTING GUIDELINE: This study was reported in accordance with the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) Statement for cross-sectional observational studies.

No patients or members of the public were directly involved in the design, conduct, analysis, or manuscript preparation of this study. The research was based on secondary analysis of publicly available and anonymized social media data.},
}

Humans
*Social Media/statistics & numerical data
Cross-Sectional Studies
Male
Female
China
*Anxiety/psychology
Emotions
Adult
*Resilience, Psychological
Digital Media
Phobic Disorders/psychology
Data Mining
Media Exposure

@article {pmid42248261,
year = {2026},
author = {Qi, H and Ruan, C and Yuan, MM and Byeon, H and Liao, J and Zhu, L and Yu, P},
title = {Longitudinal transcriptomic insights into microbial aggregation, trophic cooperation, and genomic adaptation during algal-bacterial granular sludge formation.},
journal = {Bioresource technology},
volume = {458},
number = {},
pages = {135082},
doi = {10.1016/j.biortech.2026.135082},
pmid = {42248261},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Transcriptome/genetics ; *Bacteria/genetics ; Quorum Sensing/genetics ; *Adaptation, Physiological/genetics ; Cyanobacteria/genetics ; Biofilms/growth & development ; Genome, Bacterial ; Gene Expression Profiling ; Multiomics ; Genomics ; },
abstract = {Microbial aggregates such as algal-bacterial granular sludge (ABGS) rely on tightly coordinated microbial interactions to maintain structural stability and functional performance. Despite the significance of co-assembly of phototrophs and heterotrophs in ABGS systems, the ecological and genomic succession during their formation remains poorly understood. Here, time-series multi-omics analysis was conducted to track the dynamic shifts in microbial interactions during ABGS maturation. The granulation process entailed the establishment of extensive cross-phylum nutrient exchange networks between Cyanobacteria and core heterotrophs (e.g., Pseudomonadota and Bacteroidota). Concurrently, metatranscriptomic profiling revealed a significant upregulation of genes associated with biofilm formation (e.g., rpoS, glgC, and cysE) and quorum sensing processes (e.g., yidC and secG) in Cyanobacteria as ABGS stabilized. Furthermore, the spatial densification and metabolic stabilization were accompanied by distinct shifts in community evolutionary strategies: the enrichment of energetically costly antiviral defense systems (R[2] = 0.65, P < 0.05) but decreased frequency of horizontal gene transfer (HGT). Additionally, analyses of public datasets confirmed that these structural, metabolic, and genomic patterns were conserved across diverse structured algal-bacterial communities. Collectively, our findings demonstrate how physical aggregation, trophic cooperation, and genomic adaptation co-evolve during ABGS formation, providing new insights into the ecological principles governing engineered ecosystems.},
}

*Sewage/microbiology
*Transcriptome/genetics
*Bacteria/genetics
Quorum Sensing/genetics
*Adaptation, Physiological/genetics
Cyanobacteria/genetics
Biofilms/growth & development
Genome, Bacterial
Gene Expression Profiling
Multiomics
Genomics

@article {pmid41940873,
year = {2026},
author = {Sharma, S and Khadka, A},
title = {Managing diabetes across borders and screens: mHealth use among older late-life South Asian migrants in the United States.},
journal = {Ethnicity & health},
volume = {31},
number = {6},
pages = {558-582},
doi = {10.1080/13557858.2026.2655621},
pmid = {41940873},
issn = {1465-3419},
mesh = {Humans ; United States ; South Asian People ; Aged ; *Telemedicine/statistics & numerical data ; Female ; Middle Aged ; Qualitative Research ; Male ; *Diabetes Mellitus, Type 2/therapy/ethnology ; Digital Health ; Asia, Southern/ethnology ; Interviews as Topic ; *Self-Management ; *Transients and Migrants/psychology ; Emigrants and Immigrants ; },
abstract = {OBJECTIVES: This study explores how older South Asian migrants in the United States navigate mobile health (mHealth) tools for type 2 diabetes self-management. The goal is to identify multilevel facilitators and barriers to digital engagement within culturally and structurally embedded contexts.

METHODS: We conducted a qualitative descriptive study using semi-structured interviews with 21 South Asian adults aged 55 and older who had migrated to the U.S. later in life and had recent experience using a diabetes management app. Thematic analysis was guided by the Social-Ecological Model (SEM) and the Consolidated Criteria for Reporting Qualitative Research (COREQ).

RESULTS: Participants' engagement with mHealth tools was shaped by personal confidence, emotional response, and adaptive strategies at the individual level; family and peer dynamics at the interpersonal level; lack of provider support and culturally misaligned features at the organizational level; culturally rooted norms and informal peer networks at the community level; and broader systemic exclusions related to language access, insurance coverage, and technology infrastructure at the policy level. While participants demonstrated motivation and resilience, emotional fatigue, app complexity, and cultural mismatches often limited sustained use.

CONCLUSIONS: Older South Asian migrants are not disinterested in digital health; rather, they are systemically excluded. For mHealth to meaningfully support diabetes self-management, tools and systems must be designed with linguistic access, cultural alignment, and policy-level support in mind. Findings underscore the need for culturally tailored, relationally supported, and digitally inclusive interventions that affirm the everyday realities of aging immigrant populations.},
}

Humans
United States
South Asian People
Aged
*Telemedicine/statistics & numerical data
Female
Middle Aged
Qualitative Research
Male
*Diabetes Mellitus, Type 2/therapy/ethnology
Digital Health
Asia, Southern/ethnology
Interviews as Topic
*Self-Management
*Transients and Migrants/psychology
Emigrants and Immigrants

@article {pmid42324754,
year = {2026},
author = {Kanamori, S and Sugimoto, K and Miyata, S and Nakatani, J and Nagata, T},
title = {Occupational health nurse involvement and Bright 500 certification among Japanese small- and medium-sized enterprises: a repeated cross-sectional analysis of 4 annual health and productivity management survey waves.},
journal = {Journal of occupational health},
volume = {68},
number = {1},
pages = {},
pmid = {42324754},
issn = {1348-9585},
support = {23JA2001//Japanese Ministry of Health, Labour and Welfare/ ; JSPS KAKENHI//JSPS KAKENHI/ ; 23 K16526//JSPS KAKENHI/ ; },
mesh = {Humans ; *Certification/statistics & numerical data ; Cross-Sectional Studies ; Efficiency ; *Health Promotion ; Japan ; *Occupational Health Nursing/statistics & numerical data ; *Small Business ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {OBJECTIVES: To investigate the association between occupational health nurse (OHN) involvement and Bright 500 certification, an indicator of high-performing health and productivity management (HPM), among Japanese small- and medium-sized enterprises (SMEs) using multi-year survey data.

METHODS: This observational study used secondary data from the 2021-2024 HPM Survey. Each annual response was analyzed as a corporation-year observation, and within-corporation correlation was handled with a random intercept for corporations. OHN involvement was defined as the appointment of public health nurses and/or nurses as health promotion officers. Bright 500 certification, obtained from publicly available certification records, was used as an indicator of more advanced HPM. The association was examined using a mixed-effects logistic regression model.

RESULTS: The analytical sample comprised 12 847 (2021), 14 401 (2022), 17 316 (2023), and 20 267 (2024) SMEs. OHN involvement increased from 5.1% (2021) to 5.8% (2024). Bright 500 certification was consistently higher in corporations with OHN involvement (10.8% in 2021, 8.4% in 2024) than in those without (2%-3% across years). After adjustment for survey year, region, insurer category, industry type, employee size, internal and external dissemination of HPM initiatives, and occupational physician involvement, OHN involvement was independently associated with certification (odds ratio: 2.35; 95% CI, 1.21-4.54; P = .011).

CONCLUSIONS: Across the 4 survey waves, OHN involvement was positively associated with Bright 500 certification among SMEs. These findings suggest that OHNs may be relevant to advanced HPM implementation in this setting. Future studies should capture OHN staffing arrangements, intensity and roles, and initiative timing to clarify mechanisms and potential causality.},
}

Humans
*Certification/statistics & numerical data
Cross-Sectional Studies
Efficiency
*Health Promotion
Japan
*Occupational Health Nursing/statistics & numerical data
*Small Business
Surveys and Questionnaires
Secondary Data Analysis

@article {pmid42427819,
year = {2026},
author = {Karapliafis, D and Neri, U and Olendraite, I and Charon, J and Sakaguchi, S and Hou, X and de Ridder, D and Zwart, MP and Kupczok, A},
title = {RdRpCATCH: a unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag076},
pmid = {42427819},
issn = {2631-9268},
mesh = {*RNA-Dependent RNA Polymerase/genetics ; *RNA Viruses/genetics/enzymology ; Hidden Markov Models ; *Software ; Genome, Viral ; Computational Biology/methods ; Viral Proteins/genetics ; Markov Chains ; },
abstract = {Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses rely on identifying the conserved RNA-dependent RNA polymerase (RdRp) by scanning sequencing datasets with specialized profile Hidden Markov Models (pHMMs). Recently, several new pHMM databases for RdRp detection have been released, each following distinct design principles. However, their relative performance remains unclear, and their accessibility to users without advanced computational expertise is limited. Here, we introduce the RdRp Collaborative Analysis Tool with Collections of pHMMs (RdRpCATCH: https://github.com/dimitris-karapliafis/RdRpCATCH), a platform that consolidates publicly available RdRp pHMM resources into a single, user-friendly framework. RdRpCATCH enables the scanning of (meta)transcriptomic assemblies to discover RNA viruses and provides subsequent taxonomic annotation of detected contigs. A comparative analysis of RdRp pHMM databases reveals that most are highly effective at detecting the known diversity of RNA viruses while minimizing false positives, supporting their joint use within RdRpCATCH. RdRpCATCH is distributed as both a conda package and a web server application (https://rdrpcatch.bioinformatics.nl), facilitating access for researchers with diverse levels of computational expertise. By integrating multiple pHMM resources, this unified framework addresses fragmentation in the field and reduces technical barriers, enabling comprehensive viral discovery.},
}

*RNA-Dependent RNA Polymerase/genetics
*RNA Viruses/genetics/enzymology
Hidden Markov Models
*Software
Genome, Viral
Computational Biology/methods
Viral Proteins/genetics
Markov Chains

@article {pmid42428246,
year = {2026},
author = {Wei, J and Yangsong, Q and Hongjia, R and Bingqiang, Z and Conggao, Y},
title = {From Exposure to Biomarker: Cumulative Tobacco Burden and Integrated Multiomics Signatures of High Tumor Mutational Burden in Lung Adenocarcinoma-A Secondary Analysis of the Cancer Genome Atlas.},
journal = {Human mutation},
volume = {2026},
number = {},
pages = {1906706},
pmid = {42428246},
issn = {1098-1004},
mesh = {Humans ; *Biomarkers, Tumor/genetics ; Multiomics ; *Mutation ; *Adenocarcinoma of Lung/genetics/etiology/pathology ; *Lung Neoplasms/genetics/etiology ; Female ; Male ; Middle Aged ; Smoking/adverse effects ; Aged ; Genomics/methods ; Proteomics ; },
abstract = {Environmental exposures are upstream determinants of molecular variation, yet exposure-to-biomarker gradients remain insufficiently quantified in harmonized multiomics cancer cohorts. Using TCGA lung adenocarcinoma as a model, we evaluated cumulative tobacco exposure and smoking history as determinants of variant-derived biomarkers and tested whether integrating clinical, genomic, transcriptomic, and proteomic data improves identification of high tumor mutational burden (TMB). This secondary analysis used public cBioPortal-linked TCGA data. Among 522 patients with clinical and molecular annotations, 302 ever-smokers with nonmissing pack-years, TMB, and covariates comprised the primary adjusted logistic-regression cohort, and 250 cases had matched multiomics data for prediction modeling. Higher cumulative tobacco exposure was associated with greater odds of high TMB: Compared with pack-year tertile 1, tertile 3 had an adjusted odds ratio of 2.28 (95% CI: 1.18, 4.41; p trend = 0.013), and each 10 pack-year increment was associated with an odds ratio of 1.12 (95% CI: 1.02, 1.23). Smoking categories also showed strong gradients for TMB, total nonsynonymous mutation counts, and C > A substitution fraction. Current smoking was positively associated with TP53 mutation and inversely associated with EGFR mutation relative to never-smoking. High-TMB tumors showed 201 differentially expressed transcripts and 15 differentially abundant proteins. Driver-augmented models discriminated high TMB better than broader multiomics models, although integrated scores retained prognostic relevance. These findings support exposure-aware biomarker development in lung adenocarcinoma. High TMB was defined as a cohort-specific top-quartile analytic endpoint rather than a universal clinical threshold. The findings support biomarker interpretation and hypothesis generation, not direct immunotherapy-response prediction or a clinically deployable model.},
}

Humans
*Biomarkers, Tumor/genetics
Multiomics
*Mutation
*Adenocarcinoma of Lung/genetics/etiology/pathology
*Lung Neoplasms/genetics/etiology
Female
Male
Middle Aged
Smoking/adverse effects
Aged
Genomics/methods
Proteomics

@article {pmid42429114,
year = {2026},
author = {Grafström, A and Prentius, W},
title = {Distributionally balanced sampling designs.},
journal = {Biometrics},
volume = {82},
number = {3},
pages = {},
doi = {10.1093/biomtc/ujag124},
pmid = {42429114},
issn = {1541-0420},
mesh = {Computer Simulation ; *Models, Statistical ; *Research Design ; Sampling Studies ; *Biometry/methods ; Data Interpretation, Statistical ; Ecology ; Humans ; Probability ; Sample Size ; Reproducibility of Results ; },
abstract = {We propose Distributionally Balanced Designs (DBD), a new class of probability sampling designs that target representativeness at the level of the full auxiliary distribution rather than for selected moments. In disciplines such as ecology, forestry, and environmental sciences, where field data collection is expensive, maximizing the information extracted from a limited sample is critical. More precisely, DBD can be viewed as minimum discrepancy designs that minimize the expected discrepancy between the sample and population auxiliary distributions. The key idea is to construct samples whose empirical auxiliary distribution closely matches that of the population. We present a first implementation of DBD for equal inclusion probabilities, based on an optimized circular ordering of the population and a random selection of a contiguous block of units. The ordering is chosen to minimize the design-expected energy distance, a discrepancy measure that captures differences between distributions beyond low-order moments. This criterion promotes strong spatial spread, and yields low variance for Horvitz-Thompson estimators of totals of functions that vary smoothly with respect to auxiliaries. Simulation results show that approximate DBD achieves better distributional fit than state-of-the-art methods such as the local pivotal and local cube designs. Hence, DBD can improve the reliability of estimates from costly field data, making distributional balancing effective for constructing representative surveys in resource-constrained applications.},
}

Computer Simulation
*Models, Statistical
*Research Design
Sampling Studies
*Biometry/methods
Data Interpretation, Statistical
Ecology
Humans
Probability
Sample Size
Reproducibility of Results

@article {pmid42429144,
year = {2026},
author = {Wei, L and Kong, X and Li, Y and Wu, H and Gan, Y and Sun, F},
title = {Gut dysbiosis‑derived butyrate loss predicts feeding intolerance: Multiomics evidence guiding nurse‑driven microbiota‑supportive interventions (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {3},
pages = {},
pmid = {42429144},
issn = {1791-3004},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; Multiomics ; *Gastrointestinal Microbiome ; *Butyrates/metabolism ; Critical Illness ; },
abstract = {Feeding intolerance (FI) is a common and debilitating challenge among critically ill patients that is linked to a pathway involving the collapse of the gut microbial ecology. The present review synthesizes multiomics evidence supporting a framework whereby critical illness‑associated gut dysbiosis results in a functional deficit of a microbially derived short‑chain fatty acid butyrate, a pivotal metabolite involved in maintaining intestinal barrier integrity, immuneoregulation and gastrointestinal motility. The loss of butyrate‑producing bacteria and their genetic pathways is strongly correlated with FI and may represent a contributory pathogenic mechanism. Key butyrate‑producing organisms diminished during this process include Faecalibacterium prausnitzii and Roseburia spp. Building upon this mechanistic framework, a pragmatic, nurse‑driven intervention model aimed at preserving and restoring microbial health in critically ill patients was proposed. This model is founded on four principal strategies: Minimizing iatrogenic harm (such as antibiotic/proton pump inhibitor stewardship), targeted microbiota nourishment (pre/synbiotics), cautious microbial restoration (probiotics/fecal microbiota transplantation) and innovative monitoring approaches. By integrating principles of microbial ecology with clinical nursing science, the present review provides a framework for developing nurse‑driven protocols designed to address the underlying pathophysiology of FI and improve patient outcomes.},
}

Humans
*Dysbiosis/microbiology/metabolism
Multiomics
*Gastrointestinal Microbiome
*Butyrates/metabolism
Critical Illness

@article {pmid42430437,
year = {2026},
author = {Ansari, AF and Sambamoorthy, G and Alexander, TC and Reddy, YBS and Raut, J and Dixit, NM},
title = {Quartet: Disentangling positive and negative components of microbial interactions.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014502},
doi = {10.1371/journal.pcbi.1014502},
pmid = {42430437},
issn = {1553-7358},
mesh = {*Microbiota/physiology ; *Microbial Interactions/physiology ; *Models, Biological ; Computational Biology/methods ; Computer Simulation ; Mouth/microbiology ; },
abstract = {Interspecies interactions are characterized conventionally by the net influence, positive or negative, a species exerts on another. Community ecology theories rely on these net interactions to describe the behaviour of multispecies communities. The net interactions in turn comprise positive and negative components, arising typically from cross-feeding metabolites and competition for resources. The components remain challenging to disentangle, compromising descriptions of community behaviour. Here, we devised a method to estimate the components when metabolic interactions predominate. We conceived a theoretical resource partitioning strategy which when applied to data on species growth rates disentangles the components. Consequently, the net influence a species has on another is decomposed into its positive and negative components. The interactions between a pair of species are thus defined by the 'quartet' of underlying components, specifically the positive and negative components of the net influence of each species on the other. We applied the method to 28 in silico species pairs from a representative oral microbiome and an experimental auxoptroph pair from the literature. We found that positive and negative components had comparable strengths on average. Interestingly, we found species pairs with similar net interactions but disparate components, highlighting the importance of the quartet. Further, weak net interactions could arise from cancellation of strong components. Estimating the quartet helped better understand the complex transitions in community behaviour observed upon varying resource supply in silico and in vitro. The quartet thus offers a more fundamental characterization of interspecies interactions and may help build more reliable community ecology theories, with implications for understanding and design of microbial communities.},
}

*Microbiota/physiology
*Microbial Interactions/physiology
*Models, Biological
Computational Biology/methods
Computer Simulation
Mouth/microbiology

@article {pmid42430441,
year = {2026},
author = {Arnoux, J and Mainguy, J and Bry, L and Fernandez de Grado, Q and Hoblos, Y and Vallenet, D and Calteau, A},
title = {Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1013856},
pmid = {42430441},
issn = {1553-7358},
mesh = {*Genome, Bacterial/genetics ; *Computational Biology/methods ; *Genomics/methods ; Pseudomonas aeruginosa/genetics ; *Software ; Genetic Variation ; Species Specificity ; Enterobacteriaceae/genetics ; Algorithms ; },
abstract = {Over the last decade, the expansion in the number of available genomes has profoundly transformed the study of genetic diversity, evolution, and ecological adaptation in prokaryotes. However, traditional bioinformatic approaches based on the analysis of individual genomes are showing their limitations when faced with the sheer scale of the data. To overcome these constraints, the concept of pangenome has emerged, offering a comprehensive framework to capture the full genetic repertoire of a species. In this study, we present PANORAMA, an innovative pangenomic tool designed to exploit pangenome graphs, enabling their annotation and comparison to explore the genomic diversity of several species. Based on the PPanGGOLiN pangenome graphs, PANORAMA integrates advanced methods for rule-based prediction of macromolecular systems and comparative analysis of conserved features between different pangenomes, such as spots of insertion. We illustrate the use of PANORAMA on a dataset of 941 Pseudomonas aeruginosa genomes, evaluating its performance against reference defense system prediction tools such as PADLOC and DefenseFinder. The analysis was then extended to a larger set, including four species of Enterobacteriaceae (>6,000 genomes), demonstrating PANORAMA's ability to annotate, compare, and explore the diversity and distribution of biological systems across multiple species. This work provides new methods for the large-scale comparative study of microbial genomes and highlights the relevance of pangenome approaches in deciphering their evolutionary dynamics. PANORAMA is freely available and accessible at: https://github.com/labgem/PANORAMA.},
}

*Genome, Bacterial/genetics
*Computational Biology/methods
*Genomics/methods
Pseudomonas aeruginosa/genetics
*Software
Genetic Variation
Species Specificity
Enterobacteriaceae/genetics
Algorithms

@article {pmid42423304,
year = {2026},
author = {Rehman, M and Sajjad, W and Kang, S and Rafiq, M and Zhao, Y},
title = {Mobilization of the ancient resistome from thawing permafrost.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2026.2698958},
pmid = {42423304},
issn = {1549-7828},
abstract = {Permafrost, ground frozen for at least two consecutive years, covers nearly one-quarter of the Northern Hemisphere and hosts diverse microbial communities. Climate-driven thaw is releasing preserved microorganisms and genetic material into contemporary ecosystems, where ancient genetic elements may be reintroduced into modern microbes and participate in gene exchange processes. Among these, antibiotic resistance genes (ARGs), which confer resistance to antibiotics, represent a critical yet underrecognized threat. Many originate from ancient microbial ecosystems shaped by natural antibiotic production and resistance, encode mechanisms not yet observed in clinical settings, and are associated with mobile genetic elements (MGEs) that facilitate horizontal gene transfer across microbial domains. Here, we synthesize evolutionary, molecular, and ecological perspectives on the preservation, release, and mobilization of permafrost-derived ARGs. We highlight mineral-DNA interactions that enhance the long-term stability of extracellular DNA containing ARGs and review the roles of MGEs in redistributing resistance determinants following thaw. We discuss conceptual models of rare cross-domain gene transfer and consider ecological and evolutionary implications under thawing conditions. ARG release from permafrost represents a neglected environmental factor that may contribute to antimicrobial resistance (AMR) dynamics and warrants investigation. Finally, identify key knowledge gaps and propose interdisciplinary frameworks for surveillance, risk assessment, and mitigation.},
}

@article {pmid42424242,
year = {2026},
author = {Alraihan, NM and French, M and Moore, DC and Sedda, L},
title = {Public health informatics tools for dengue risk management: A systematic review.},
journal = {PLOS digital health},
volume = {5},
number = {7},
pages = {e0001495},
pmid = {42424242},
issn = {2767-3170},
abstract = {Public health informatics (PHI) tools, including Geographic Information Systems (GIS), Electronic Health Records (EHRs), and Health Information Exchange systems, are increasingly applied to dengue fever surveillance, prevention, and control. Despite their growing adoption, a synthesis of empirical evidence examining their real-world application across endemic settings has not previously been conducted. This systematic review aimed to examine how PHI tools have been applied to dengue risk management, and to evaluate the certainty of evidence supporting their use. A structured literature search was conducted across PubMed, EBSCO/MEDLINE, and Web of Science. Nineteen peer-reviewed empirical studies published between 2010 and 2024 were included following eligibility screening against pre-defined inclusion and exclusion criteria. Study quality was assessed using the Newcastle-Ottawa Scale adapted for cross-sectional studies. Certainty of evidence was evaluated using the GRADE framework across five domains: risk of bias, inconsistency, indirectness, imprecision, and publication bias. Findings were synthesised narratively and organised into three functional categories: mapping and visualisation (n = 12), epidemiological insights (n = 5), and enhanced surveillance (n = 2). GIS was the most frequently used tool, consistently identifying dengue hotspots and supporting spatial dengue risk mapping across diverse geographic settings. EHR-linked health information systems supported epidemiological profiling and, in a limited number of studies, improved outbreak detection. Certainty of evidence was rated as very low across all three categories, reflecting the low evidence associated to observational study designs, methodological heterogeneity, and the uniform reporting of positive findings across all included studies. PHI tools show consistent descriptive utility in dengue surveillance across diverse settings. However, given the very low certainty of evidence, conclusions should be interpreted with caution. Gaps remain in high-burden regions including Sub-Saharan Africa and the Middle East. Standardised evaluation frameworks, broader geographic representation, and integration with emerging digital health technologies are needed to strengthen the evidence base. Systematic review registration: PROSPERO; registration number CRD42024572021.},
}

@article {pmid42426003,
year = {2026},
author = {Lei, Z and Liu, H and Zhang, Y and Li, X and Xiao, C and Xing, G and Guo, R and Zhang, Y and Xu, J and Yang, W and Chen, H and Li, M and Lu, T and Li, S and Lu, Y and Yan, Q},
title = {The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01088-3},
pmid = {42426003},
issn = {2055-5008},
support = {32202857//National Natural Science Foundation of China/ ; 2024BBB073//Hubei Key Research and Development Project/ ; YXYX2506//Open Research Project of Sichuan Provincial Clinical Research Center for Imaging Medicine/ ; XN202402//Open Project of Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education/ ; 2022CXRC9555//Ganzhou Science and Technology Innovation Talent Project - Youth Talent Project/ ; },
abstract = {The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.},
}

@article {pmid41861125,
year = {2026},
author = {Hopkins, B and Davies, P and Noble, PJ and Bunford-Davies, A and Lawson, A and Pinchbeck, G and Lloyd, I and Smith, R and Radford, AD},
title = {Reusing health records from farm animal practices at scale: A potential complementary method of surveillance.},
journal = {The Veterinary record},
volume = {199},
number = {2},
pages = {e73-e81},
doi = {10.1002/vetr.70501},
pmid = {41861125},
issn = {2042-7670},
support = {//Welsh Government/ ; //Llywodraeth Cymru/ ; //Arwain DGC/ ; },
mesh = {Animals ; Cattle ; Sheep ; *Electronic Health Records/statistics & numerical data ; *Sheep Diseases/drug therapy/epidemiology ; *Cattle Diseases/drug therapy/epidemiology ; Wales/epidemiology ; Pilot Projects ; Data Mining ; Anti-Bacterial Agents/therapeutic use ; *Population Surveillance/methods ; Animals, Domestic ; Farms ; },
abstract = {BACKGROUND: Disease in primary care frequently represents a surveillance blind spot, particularly for diseases affecting farm animals.

METHODS: Electronic health records (EHRs) were collected from four farm animal veterinary practices in Wales (February 2024‒January 2025) as part of a pilot study. Information collected included species treated, date, owner postcode, products sold and clinical free text. Text mining and topic modelling were used to describe treatments and classify syndromes.

RESULTS: In total, 32,799 records were collected. Antimicrobials were prescribed in 32.6% and 63.8% of cattle and sheep records, respectively. The most frequent antibiotic classes in both species were tetracyclines, macrolides, penicillins and penicillin‒aminoglycoside combinations. There were no recorded category A antimicrobials, and category B antimicrobials were prescribed in only 0.12% and 0.04% of cattle and sheep EHRs, respectively. Text mining and topic modelling seemed efficient methods to identify key syndromes, including mastitis, joint ill, lameness and pneumonia, and how these were treated.

LIMITATIONS: Some EHRs described more than one animal with different diagnoses, obfuscating the attribution of treatment to syndrome.

CONCLUSION: The increasing availability of EHRs at scale and in real-time represents a complementary opportunity to survey disease and treatment on farms. Text mining methods, including artificial intelligence, could efficiently identify important syndromes and provide novel insight into use of antibacterials.},
}

Animals
Cattle
Sheep
*Electronic Health Records/statistics & numerical data
*Sheep Diseases/drug therapy/epidemiology
*Cattle Diseases/drug therapy/epidemiology
Wales/epidemiology
Pilot Projects
Data Mining
Anti-Bacterial Agents/therapeutic use
*Population Surveillance/methods
Animals, Domestic
Farms

@article {pmid42049773,
year = {2026},
author = {Wei, X and Tang, D and Peng, Y and Huang, B and Zhu, Y and Liang, Z and Hu, Y},
title = {A telomere-to-telomere reference genome for Stemona tuberosa.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42049773},
issn = {2052-4463},
mesh = {*Genome, Plant ; Haplotypes ; *Stemonaceae/genetics ; *Telomere/genetics ; Datasets as Topic ; },
abstract = {Stemona tuberosa is a medicinally important species, however, a complete telomere-to-telomere (T2T) genome assembly has remained unavailable. Here, we present the first T2T genome assembly for S. tuberosa, generated by integrating PacBio HiFi, ultra-long Oxford Nanopore, Illumina, and Hi-C sequencing technologies. The assembly produced two highly contiguous haplotype-resolved genomes, with total sizes of 803.04 Mb and 795.04 Mb, and contig N50 values of 113.29 Mb and 111.11 Mb, respectively. The proportion of fully assembled chromosomes reached 100% in both haplotypes. In addition, 14 putative centromeric regions were successfully identified across 7 pseudochromosomes, along with the annotation of 25,561 and 25,854 genes in the two haplotypes, respectively. This T2T genome assembly of S. tuberosa provides a valuable reference for elucidating the genetic architecture of the species. It significantly advances our capacity to investigate structural variations, gene function, and evolutionary processes within Stemona and related medicinal plant lineages.},
}

*Genome, Plant
Haplotypes
*Stemonaceae/genetics
*Telomere/genetics
Datasets as Topic

@article {pmid42056141,
year = {2026},
author = {Li, W and Yu, D and Que, Y and Tian, H and Dong, W and Wang, E and Xu, N and Shao, K and Zhu, B and Hu, X},
title = {The first chromosomal level genome assembly and annotation of Pareuchiloglanis anteanalis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42056141},
issn = {2052-4463},
support = {31572593//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Catfishes/genetics ; *Chromosomes ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Pareuchiloglanis anteanalis belonging to the genus Pareuchiloglanis, within the family Sisoridae (order Siluriformes), is a group of small benthic-dwelling freshwater fishes adapted to alpine canyon environments characterized by steep slopes, rapid currents, and marked seasonal fluctuations in water discharge between dry and flood periods. This species is primarily distributed in the Jinsha River, Dadu River, and Bailong River, all located within the upper reaches of the Yangtze River drainage. In this research, through the integration of PacBio HiFi long read sequencing and Hi-C (high-throughput chromatin capture) technology, we generated a high-quality chromosome-level genome of the P. anteanalis. The assembly yielded a genome of 873.97 Mb, with a scaffold N50 length of 50.12 Mb, covering 98.59% of the contig-level genome, were accurately mapped onto 18 chromosomes by using Hi-C data. The BUSCO analysis indicated that the completeness of the genome assembly and the annotation both reached 93.3% and 93.4%, respectively. This high-quality genomic resource provides a solid foundation for deciphering genome architecture and functional elements, thereby enabling deeper investigations into the genetic mechanisms underlying adaptation in P. anteanalis. Moreover, it offers valuable support for resource conservation, artificial propagation, and selective breeding of this native species.},
}

Animals
*Catfishes/genetics
*Chromosomes
*Genome
Molecular Sequence Annotation
Datasets as Topic

@article {pmid42106342,
year = {2026},
author = {Mateo, M and Briand, C and Korta, M and Beaulaton, L and Drouineau, H and Pella, H and Amilhat, E and Bardonnet, A and Antunes, C and De Miguel Rubio, R and Domingos, I and Fernández-Delgado, C and Labedan, M and Herrera, M and Sagnes, P and Zamora, L and Díaz, E},
title = {A database of eels and their freshwater habitats in southwestern Europe.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42106342},
issn = {2052-4463},
mesh = {Animals ; *Ecosystem ; Rivers ; *Anguilla ; Fresh Water ; Spain ; Portugal ; Animal Migration ; France ; Databases, Factual ; },
abstract = {The European eel stock (Anguilla anguilla) is outside safe biological limits. A range-wide stock assessment requires the creation and standardisation of databases that include information on eels and their habitats in different countries throughout their distribution range. The SUDOANG 1.0.4 database compiles standardised data on river courses in France and the Iberian Peninsula (Spain and Portugal). Using GIS tools, information on water surface and on other potential aquatic habitats surrounding each river segment has been collected. This common river network provides tools to quickly accumulate information along the river or along the natural path of migration from/to the sea. The database also compiles information on the surface of other habitats, human pressures (including 106400 obstacles), and provides eel abundance and biometric estimations derived from the Eel Density Analysis (EDA) model at the river reach scale for the reference year 2015. The river network supports ecological assessment of the eel habitats, and should also be useful for studies on other migratory species.},
}

Animals
*Ecosystem
Rivers
*Anguilla
Fresh Water
Spain
Portugal
Animal Migration
France
Databases, Factual

@article {pmid42174524,
year = {2026},
author = {Yuan, M and Bi, S and Chen, Z and Fan, X and Chen, X and Shen, K},
title = {Development of an interpretable machine learning model-based online tool for risk prediction of falls and fall-related injuries in Chinese middle-aged and older adults with depressive symptoms-a longitudinal study based on the CHARLS database.},
journal = {BMC public health},
volume = {26},
number = {1},
pages = {},
pmid = {42174524},
issn = {1471-2458},
mesh = {Humans ; *Accidental Falls/statistics & numerical data ; China/epidemiology ; Longitudinal Studies ; Middle Aged ; Predictive Learning Models ; *Wounds and Injuries/epidemiology ; *Depression/epidemiology ; Risk Assessment/methods ; Aged ; Female ; Male ; *Machine Learning ; Boosting Machine Learning Algorithms ; Databases, Factual ; Prediction Algorithms ; East Asian People ; },
abstract = {BACKGROUND: This study aimed to establish and validate interpretable Machine Learning (ML) models for predicting falls and fall-related injuries in middle-aged and older adults with depressive symptoms (DS) and to develop relevant online computational tools.

METHODS: Using data from the China Health and Retirement Longitudinal Study (CHARLS) survey from 2015 to 2018, 32 predictor variables related to the risk of falls and fall-related injuries in middle-aged and older adults with DS were included based on five dimensions of the health ecology model, and the important predictor variables were screened using Principal Component Analysis and LASSO regression at the same time. We further developed eight ML algorithms-Logistic Regression(LR), Support Vector Machine(SVM), Gradient Boosting Machine (GBM), Neural Network (NN), eXtreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), Light Gradient Boosting Machine (LightGBM) and Categorical Boosting (CatBoost)-to construct the risk prediction model, and selected the best predictive variables based on grid search and 10-fold cross-validation. SHapley Additive exPlanations (SHAP) was used for personalised interpretation of the models. In addition, we further performed stratified analyses by dividing participants into two age groups: 45-59 years and 60 years and older.

RESULTS: Among 3,664 middle-aged and older adults with DS, the incidence rate of falls and fall-related injuries after three years of follow-up was 20.36% and 8.92%, respectively. Among all models, LightGBM had the best performance. LightGBM performed the best, with an area under the curve (AUC) of 0.821 (95% CI: 0.802-0.841) for the fall risk test set and an AUC of 0.905 (95% CI: 0.892-0.919) for the fall injury risk test set. We identified important risk factors for falls and fall-related injuries in middle-aged and older adults with DS. The optimal predictive model and risk predictors differed from those identified before stratification by age. SHAP visualises the specific contributions of these risk factors, thereby enhancing the model's value for application. Online tools to implement the model are available at https://riskpredictiontool.shinyapps.io/falls_prediction_tool/ and https://riskpredictiontool.shinyapps.io/fall_related_injuries_prediction_tool/.

DISCUSSION AND CONCLUSIONS: The results can help predict risk of falls and fall-related injuries among middle-aged and older adults with DS. These findings provide an important guide for the development of public health strategies.},
}

Humans
*Accidental Falls/statistics & numerical data
China/epidemiology
Longitudinal Studies
Middle Aged
Predictive Learning Models
*Wounds and Injuries/epidemiology
*Depression/epidemiology
Risk Assessment/methods
Aged
Female
Male
*Machine Learning
Boosting Machine Learning Algorithms
Databases, Factual
Prediction Algorithms
East Asian People

@article {pmid42418234,
year = {2026},
author = {Araujo Serrao de Andrade, A and Silverj, A and Josephs, T and Gregory, AC},
title = {Evolving strategies for virus discovery.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
pmid = {42418234},
issn = {2057-5858},
mesh = {*Viruses/genetics/isolation & purification/classification ; Genome, Viral ; *Metagenomics/methods ; *Virome/genetics ; Artificial Intelligence ; Computational Biology/methods ; },
abstract = {Viruses interact with all domains of life and play fundamental roles in shaping biological systems from individual hosts to global ecosystems. Yet their identification remains difficult due to a lack of a universal marker gene and the extensive diversity of viral genomes. Despite this, the speed of viral discovery is quickly increasing, driven by the growing number of virome studies, improved sequencing technologies and the decreased cost of sequencing. In this review, we examine the evolution of virus identification approaches from classical and molecular methods to contemporary genome-resolved and computational frameworks. By aggregating genome-resolved virome studies from 2010 to early 2026 that meet defined criteria (n=502), we synthesize the current landscape of virus identification methods, including similarity-based, sequence-based artificial intelligence (AI) and hybrid approaches. We also highlight the key limitations of the current methods, particularly biases in reference databases that contribute to persistent viral 'dark matter'. Finally, we identify emerging opportunities for the field in structure-based and AI-driven approaches that extend detection beyond sequence similarity and outline how these integrative frameworks are poised to improve virus discovery across ecosystems.},
}

*Viruses/genetics/isolation & purification/classification
Genome, Viral
*Metagenomics/methods
*Virome/genetics
Artificial Intelligence
Computational Biology/methods

@article {pmid42419831,
year = {2026},
author = {Li, JW and Wang, Y and Chaurasia, A},
title = {Microbial biomarkers for OPMD progression.},
journal = {Advances in immunology},
volume = {169},
number = {},
pages = {193-212},
doi = {10.1016/bs.ai.2026.03.001},
pmid = {42419831},
issn = {1557-8445},
mesh = {Humans ; *Microbiota ; Disease Progression ; *Mouth Neoplasms/microbiology/diagnosis ; *Dysbiosis/microbiology ; Biomarkers ; *Carcinoma, Squamous Cell/microbiology/diagnosis ; *Biomarkers, Tumor ; *Precancerous Conditions/microbiology ; Metabolomics ; Multiomics ; },
abstract = {Oral potentially malignant disorders (OPMDs) present a heterogeneous risk of progression to oral squamous cell carcinoma (OSCC), underscoring the need for reliable, non-invasive biomarkers to aid in clinical stratification. This chapter evaluates the utility of the oral microbiome as a source of predictive biomarkers for OPMD progression. Current evidence indicates that OPMDs and OSCC are frequently associated with microbial dysbiosis, characterized by a shift toward anaerobic, periodontal-associated taxa, such as Fusobacterium and Porphyromonas, and a concomitant depletion of health-associated Streptococcus. However, translating these taxonomic signatures into clinical practice is hindered by overlapping community structures across healthy, premalignant, and malignant mucosal states, alongside significant confounding from periodontal inflammation and lifestyle exposures. Furthermore, the field remains divided on whether this dysbiosis acts as an upstream driver of carcinogenesis or a downstream consequence of tumor-associated microenvironmental selection. To overcome these methodological and biological limitations, this chapter advocates for an ecology-driven, multi-omics approach. By integrating taxonomic profiling with functional readouts like metabolomics and metaproteomics, and contextualizing these signals within host microenvironmental strata (e.g., hypoxia and inflammation), researchers can achieve greater mechanistic interpretability and robustness. Ultimately, microbiome-informed tools are best positioned not as standalone diagnostic tests, but as adjunctive instruments for clinical triage and risk enrichment, provided they are rigorously validated in prospective, longitudinal converter/non-converter cohorts.},
}

Humans
*Microbiota
Disease Progression
*Mouth Neoplasms/microbiology/diagnosis
*Dysbiosis/microbiology
Biomarkers
*Carcinoma, Squamous Cell/microbiology/diagnosis
*Biomarkers, Tumor
*Precancerous Conditions/microbiology
Metabolomics
Multiomics

@article {pmid42422686,
year = {2026},
author = {Lyu, Y and Luo, C},
title = {Digital access, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China: media-use ecologies and cross-sectional associations.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1794204},
pmid = {42422686},
issn = {2296-2565},
mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; China ; Adult ; *Rural Population/statistics & numerical data ; Middle Aged ; Digital Health ; Digital Media ; Self Report ; *Health Behavior ; Media Exposure ; Adolescent ; Young Adult ; Aged ; },
abstract = {BACKGROUND: Digital health education may help reduce health-information inequality in underdeveloped rural areas, but evidence remains limited on how rural residents encounter health information across different media environments and how digital access, usability, engagement, and self-reported preventive behavior are interrelated. This study examined media-use ecologies and cross-sectional associations among digital access and skills, digital health information engagement, and self-reported preventive behavior among rural adults in Guizhou, China.

METHODS: A cross-sectional survey was conducted among 1,265 adult rural residents recruited from five selected counties/districts in Guizhou Province using a multistage non-probability sampling design. Latent class analysis was used to characterize health-information media-use ecologies based on nine indicators of information channels and social media platforms. Regression-based cross-sectional association models examined associations among digital access and skills, perceived ease of understanding digital health content, lower operational difficulty, digital health information engagement, attitudes and willingness toward health education, and self-reported preventive behavior, adjusting for sex, age, education, income, and media-use ecology.

RESULTS: Five media-use ecologies were identified, reflecting different combinations of offline interpersonal/professional channels, traditional media, and digital platforms. Residents in omnichannel and short-video/social-platform-centered ecologies reported higher digital health information engagement, whereas those in the offline village doctor/traditional channels ecology reported the lowest engagement. Higher digital access and skills were associated with stronger engagement, and this association was attenuated after accounting for perceived ease of understanding and lower operational difficulty. Greater engagement was associated with more frequent self-reported preventive behavior, and this association was attenuated after accounting for attitudes toward health education and willingness to adopt new forms of health education.

CONCLUSION: In this non-probability adult sample from selected rural sites in Guizhou, digital health inequality was reflected not only in unequal access to devices and networks, but also in differences in understanding, usability, engagement, and self-reported preventive behavior. The findings should be interpreted as cross-sectional associations among field-feasible indicators rather than evidence of causal mechanisms.},
}

Humans
Cross-Sectional Studies
Female
Male
China
Adult
*Rural Population/statistics & numerical data
Middle Aged
Digital Health
Digital Media
Self Report
*Health Behavior
Media Exposure
Adolescent
Young Adult
Aged

@article {pmid41543584,
year = {2026},
author = {Gupta, S and Patil, AB and Soman, AS and Vijay, N},
title = {Master of none: GPRC6A gene loss is more widespread than previously known.},
journal = {Genetica},
volume = {154},
number = {1},
pages = {5},
pmid = {41543584},
issn = {1573-6857},
support = {B.T./11/IYBA/2018/03//Department of Biotechnology, Ministry of Science and Technology, India/ ; E.C.R./2017/001430//Science and Engineering Research Board/ ; },
mesh = {*Receptors, G-Protein-Coupled/genetics ; *Mammals/genetics ; Humans ; Animals ; *Synteny ; *Evolution, Molecular ; Genome ; Datasets as Topic ; },
abstract = {GPRC6A encodes a class C GPCR that can be activated by multiple ligands and potentially acts as a central regulator of diverse metabolic processes by modulating endocrine pathways. Experimental studies have reported numerous distinct functions for GPRC6A, suggesting it may be a key drug target for several metabolic disorders. Yet, the actual function of GPRC6A has been the focus of considerable debate due to contradictory results and the prevalence of loss-of-function mutations in human populations, leading to the perception of GPRC6A as a "Master of none". Interestingly, a genome-wide screen for gene loss events in vertebrate species identified the disruption of the GPRC6A gene in toothed whales, in contrast to widespread conservation in the closely related Bovidae family. We employ a synteny-informed comparative genomic approach to demonstrate that the loss of the GPRC6A gene among mammalian species is more widespread than previously reported, encompassing the entire Bovidae group within Artiodactyla and other fully aquatic mammals, including those belonging to Sirenia. An in-depth search of the genomes and short and long-read sequencing datasets of monotremes, hystricomorphs, rhinolophoid bats, pika, koala, and two shrews (white-toothed pygmy shrew and Asian house shrew) reveals at least nine independent GPRC6A gene loss events in vertebrates, highlighting its lineage-specific dispensability and raising questions regarding its ubiquitous functionality. The evolutionary loss of GPRC6A likely represents a lineage-specific response to specialised diets and ecological niches, reshaping metabolic regulation and taste perception and illuminating how niche specialisation influences gene retention or loss within the GPCR landscape across species.},
}

*Receptors, G-Protein-Coupled/genetics
*Mammals/genetics
Humans
Animals
*Synteny
*Evolution, Molecular
Genome
Datasets as Topic

@article {pmid41921848,
year = {2026},
author = {Xu, H and Sun, J and Lu, F and Luo, Y and Bie, L and Xia, Q and Wang, Y and Lin, P and Shen, G},
title = {IMDD: A Database for Exploring Tissue-Specific Gene Expression Dynamics During Holometabolous Insects.},
journal = {Journal of molecular biology},
volume = {438},
number = {18},
pages = {169781},
doi = {10.1016/j.jmb.2026.169781},
pmid = {41921848},
issn = {1089-8638},
mesh = {Animals ; *Metamorphosis, Biological/genetics ; *Gene Expression Regulation, Developmental ; *Databases, Genetic ; Drosophila melanogaster/genetics/growth & development ; *Holometabola/genetics/growth & development ; Bombyx/genetics/growth & development ; Transcriptome/genetics ; Biocuration ; Organ Specificity/genetics ; Gene Regulatory Networks ; Bees/genetics/growth & development ; },
abstract = {The intricate process of insect metamorphosis is governed by precise tissue-specific gene expression dynamics. To facilitate the exploration of these complex regulatory programs, we have developed the Insect Metamorphic Development Database (IMDD), an interactive platform for four key holometabolous species, including Drosophila melanogaster, Bombyx mori, Aedes aegypti and Apis mellifera, which hold significant ecological, economic, and medical importance. IMDD integrates over 1200 bulk-tissue transcriptomes and more than 1.4 million single-cell profiles, providing broad coverage of developmental stages. The platform is specifically designed to empower researchers to explore dynamic gene expression changes at both tissue and single-cell resolutions, investigate cellular heterogeneity, and trace cell-type transitions. By providing a user-friendly interface for dissecting the molecular underpinnings of insect development, IMDD serves as a critical resource for exploring the spatiotemporal gene regulatory networks that drive metamorphosis. The database is freely accessible at http://www.bioimdd.com/.},
}

Animals
*Metamorphosis, Biological/genetics
*Gene Expression Regulation, Developmental
*Databases, Genetic
Drosophila melanogaster/genetics/growth & development
*Holometabola/genetics/growth & development
Bombyx/genetics/growth & development
Transcriptome/genetics
Biocuration
Organ Specificity/genetics
Gene Regulatory Networks
Bees/genetics/growth & development

@article {pmid42050343,
year = {2026},
author = {Sun, H and Wang, X and Deng, H and Xie, L and Zhou, E and Tan, N and Wu, Y},
title = {The chromosome-level genome assembly and annotation of Parabotia bimaculata (Cypriniformes: Cobitidae: Botiinae).},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42050343},
issn = {2052-4463},
support = {KJZD-M202401301//Major Science and Technology Research Project of Chongqing Municipal Education Commission/ ; R2022YS08//Tower Foundation Program of Chongqing University of Arts and Sciences in China/ ; },
mesh = {Animals ; *Chromosomes ; *Cypriniformes/genetics ; *Genome ; Molecular Sequence Annotation ; Datasets as Topic ; },
abstract = {Parabotia bimaculata is a rare loach species endemic to southwestern China. A high-quality reference genome is essential for advancing research across various biological fields concerning this species. Here, we report the first chromosome-level genome assembly and annotation of P. bimaculata. The assembled genome spans 610.59 Mb with a contig N50 of 21.19 Mb. Hi-C scaffolding anchored 96.92% of the sequences into 25 pseudo-chromosomes. By integrating homology-based prediction with RNA-sequencing data, we identified 26,312 protein-coding genes, of which 23,833 (90.58%) were functionally annotated. The assembly achieved a 98.54% BUSCO completeness score. This work provides a valuable genomic resource for P. bimaculata, establishing a foundation for future studies in genomics, evolutionary biology, and conservation.},
}

Animals
*Chromosomes
*Cypriniformes/genetics
*Genome
Molecular Sequence Annotation
Datasets as Topic

@article {pmid42143165,
year = {2026},
author = {Yang, J and Liang, BY and Fang, CY and Li, JJ and Zhang, P and Xiang, P and Zhang, LW and Liu, H},
title = {Exploring dysregulation of cuproptosis-related genes molecular clusters and candidate biomarkers in pterygium.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42143165},
issn = {2045-2322},
support = {ZKF2024042//National clinical key specialty ophthalmology open foundation/ ; ZKF2024041//National clinical key specialty ophthalmology open foundation/ ; 82560205//National Natural Science Foundation of China/ ; 82460201//National Natural Science Foundation of China/ ; 202208535051//China Scholarship Council/ ; 24JCQNJC02050//Tianjin Natural Science Foundation/ ; YDYXJJ2024-0003//Yunnan University Medical Research Foundation/ ; 2024YNLCYXZX0343//Key Project of the Provincial Clinical Center of Yunnan Province/ ; },
mesh = {Humans ; *Pterygium/genetics/pathology/immunology/metabolism ; *Cuproptosis/genetics ; Biomarkers/metabolism ; Gene Expression Profiling ; Transcriptome ; Female ; Gene Expression Regulation ; Male ; Computational Biology/methods ; Machine Learning ; },
abstract = {Pterygium is a common ocular surface disorder, with its prevalence strongly correlated to ultraviolet (UV) exposure in geographic regions. Epidemiological investigations reveal significant demographic variations, with higher incidences observed in areas with intense UV radiation and within specific populations, notably rural individuals. Despite surgical interventions being the standard treatment, recurrent cases underline the necessity for understanding the underlying biological mechanisms contributing to pterygium pathogenesis. Recent advancements in cellular death mechanisms point to cuproptosis, a copper-dependent programmed cell death pathway, as a potential regulatory factor in ocular diseases, including pterygium. This study aims to systematically investigate the immunological significance of cuproptosis-related genes (CuRGs) in pterygium's pathogenesis using an integrative bioinformatics framework. We performed transcriptomic profiling on pterygium tissues and employed machine learning algorithms to identify pivotal biomarkers for pterygium risk stratification. Comprehensive immune profiling and functional enrichment analyses were conducted to elucidate the interplay between identified CuRGs and the immune microenvironment in pterygium. Our analysis highlighted 19 CuRGs, with eight genes displaying significant dysregulation in pterygium tissues (p < 0.05). We established robust associations between CuRG expression and prominent immune cell infiltrates, notably regulatory T cells and macrophages. Furthermore, three core biomarkers (SERTAD1, JMJD1C, CSRNP1) were identified through machine learning and validated by QPCR, with the support vector machine model demonstrating exceptional predictive performance (AUC = 0.84). Empirical validation corroborated significant downregulation of selected biomarkers in pterygium tissue samples compared to normal conjunctiva. Our findings underscore the vital role of CuRGs in modulating pterygium development through immune and metabolic interactions, establishing their potential as novel therapeutic targets. Nevertheless, our study has limitations, as these findings are hypothesis-generating and require validation in larger patient cohorts.},
}

Humans
*Pterygium/genetics/pathology/immunology/metabolism
*Cuproptosis/genetics
Biomarkers/metabolism
Gene Expression Profiling
Transcriptome
Female
Gene Expression Regulation
Male
Computational Biology/methods
Machine Learning

@article {pmid42263834,
year = {2026},
author = {Veli-Quispe, D and Urquizo-Prado, S and Cesare-Ariza, E and Ybaseta-Medina, J and Panay-Centeno, J and Tasayco-Márquez, LM and Ubillus, M and Montoya, Y and Torres-Roman, JS},
title = {Trends and regional inequalities in cerebrovascular disease mortality in Peru: An ecological time-series analysis, 2017-2025.},
journal = {Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association},
volume = {35},
number = {8},
pages = {108675},
doi = {10.1016/j.jstrokecerebrovasdis.2026.108675},
pmid = {42263834},
issn = {1532-8511},
mesh = {Humans ; Peru/epidemiology ; *Cerebrovascular Disorders/mortality/diagnosis ; Female ; Male ; Time Factors ; Risk Factors ; *Health Status Disparities ; Aged ; Databases, Factual ; Middle Aged ; Risk Assessment ; Sex Distribution ; *Rural Health ; Cause of Death/trends ; Adult ; Age Distribution ; Socioeconomic Disparities in Health ; Urban Health ; Sex Factors ; Aged, 80 and over ; },
abstract = {BACKGROUND: Cerebrovascular disease remains a leading cause of mortality worldwide. In Peru, evidence on recent mortality trends and regional disparities is limited.

OBJECTIVE: To evaluate temporal trends and regional disparities in cerebrovascular disease mortality in Peru between 2017 and 2025.

METHODS: An ecological time-series study was conducted using national mortality data from the National Death Information System (SINADEF). Deaths with cerebrovascular disease as the underlying cause (ICD-10: I60-I69) were included. Age-standardised mortality rates (ASMRs) per 100,000 person-years were calculated using the SEGI world standard population. Temporal trends were analyzed using Joinpoint regression models to estimate annual percent change (APC) and average annual percent change (AAPC) with 95% confidence intervals (95% CI).

RESULTS: National cerebrovascular disease mortality rates remained relatively stable between 2017 and 2025 in both men and women. However, marked regional disparities were identified. The highest mortality rates were concentrated in Huancavelica, San Martín, and Apurímac. Among men, a significant increase was identified in Huanuco (APC: 7.6%; 95% CI: 2.6 to 12.9), whereas significant decreasing trends were observed in Lambayeque (APC: -8.0%; 95% CI: -14.0 to -1.6), Madre de Dios (APC: -5.9%; 95% CI: -11.3 to -0.2), Tacna (APC: -5.8%; 95% CI: -9.7 to -1.7), and Tumbes (APC: -5.9%; 95% CI: -10.7 to -0.9). Among women, Huanuco also showed a significant increase (APC: 7.0%; 95% CI: 4.0 to 10.1), while significant decreasing trends were identified in Callao (APC: -5.3%; 95% CI: -8.2 to -2.3), La Libertad (APC: -5.7%; 95% CI: -11.0 to -0.02), Moquegua (APC: -8.6%; 95% CI: -14.0 to -2.9), and Tacna (APC: -6.5%; 95% CI: -11.2 to -1.5).

CONCLUSION: Cerebrovascular disease mortality in Peru remained relatively stable at the national level but showed important regional heterogeneity. These findings highlight geographic disparities in mortality patterns and underscore the need for further research and region-specific public health strategies to improve cerebrovascular disease prevention and care.},
}

Humans
Peru/epidemiology
*Cerebrovascular Disorders/mortality/diagnosis
Female
Male
Time Factors
Risk Factors
*Health Status Disparities
Aged
Databases, Factual
Middle Aged
Risk Assessment
Sex Distribution
*Rural Health
Cause of Death/trends
Adult
Age Distribution
Socioeconomic Disparities in Health
Urban Health
Sex Factors
Aged, 80 and over

@article {pmid42395566,
year = {2026},
author = {Formenti, G and Absolon, DE and Abueg, LAL and Ackerman, F and Al-Ajli, FO and Aleixo, A and Antunes, A and Arcila, D and Audet, JN and Balacco, JR and Beavan, AJS and Belov, K and Betancur-R, R and Bidwell, SL and Biegler, MT and Bista, I and Blaxter, M and Boyer, K and Braasch, I and Bradbury, IR and Brajuka, N and Bronikowski, AM and Brown, T and Butler, G and Cao, S and Charvel, E and Chen, Y and Ciofi, C and Clawson, HM and Collins, JC and Correard, S and Corrigan, S and Couture, M and Crawford, AJ and D'Alessandre, ND and da Conceicao, HB and da Fonseca, RR and Daigavane, M and Dalapicolla, J and de Bruyn, M and de Jong, E and De Panis, DN and Detrich, HW and Scott, CD and Diekhans, M and Duarte, E and Durbin, R and Escalona, M and Eschenbrenner, M and Fedrigo, O and Fenn, J and Flannery, P and Forde, N and Gable, SM and Galante, PA and Ganesan, R and Gardiner, A and Garrison, E and Gemmell, NJ and Gilbert, MTP and Giudicelli, F and Gonçalves, TM and Guardia, GDA and Guarracino, A and Gupta, A and Haase, B and Hays, D and Hickey, G and Hiller, M and Hime, PM and Hogg, CJ and Horan, KM and Howe, K and Jackson, D and Jain, N and Kang, L and Kliver, S and Ko, BJ and Koepfli, KP and Komissarov, A and Komoroske, LM and Koo, B and Koren, S and Korlach, J and Kovacic, I and Krasheninnikova, K and Kuderna, LF and Langlois, RA and Lariviere, D and Larkin, DM and Lee, C and Lee, YH and Lewin, HA and Lim, D and Lou, RN and Mak, SS and Makova, KD and Marín-Gual, L and Marques-Bonet, T and Martin, FJ and Mathers, TC and Mazzoni, CJ and McCaffrey, K and McCarthy, SA and Medico, JA and Mercuri, RLV and Meyer, A and Michalak, P and Mirarab, S and Morin, PA and Mountcastle, J and Murphy, RW and Murphy, TD and Myers, EW and Naylor, GJ and Near, T and Nekrutenko, A and Ning, Z and Novak, BJ and O'Brien, MF and O'Connell, MJ and O'Toole, BP and Paez, S and Paten, B and Paulini, M and Pelan, SE and Pennell, M and Pfenning, AR and Phillippy, AM and Pinto, B and Pippel, M and Popova, M and Prylutskyi, M and Rhie, A and Crollius, HR and Ruiz-Herrera, A and Ryder, O and Safonova, Y and Santos, CA and Schatz, MC and Secomandi, S and Shaffer, HB and Shalmiyev, L and Shapiro, B and Smith, JJ and Sollitto, M and Sotero-Caio, CG and Steiner, CC and Sudmant, PH and Sweeney, DJ and Talbot, SC and Taylor, CH and Teeling, EC and Thibaud-Nissen, F and Tilley, T and Timoshevskaya, N and Traore, P and Turakhia, Y and Uliano-Silva, M and Venditti, C and Venkatesh, B and Vernes, SC and Warren, WC and Whelan, CV and Wilson, MA and Winkler, S and Wood, JM and Zhang, G and Zhao, G and Jarvis, ED and , },
title = {The Vertebrate Genomes Project Phase I: A global reference genome resource.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42395566},
issn = {2692-8205},
abstract = {The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ~70,000 extant vertebrate species[1]. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ~95% of vertebrate orders, along with additional lineages within those orders, totaling 816 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods[2-4], alongside the growth of associated consortium initiatives and international collaborations[5-9]. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers a reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.},
}

@article {pmid42400857,
year = {2026},
author = {Meng, Q and Ma, M and Li, S and Han, X and Jin, T and Jiao, Y and Wang, L},
title = {Structural Variability in Bulk Soil and Rhizosphere Microbial Communities at Different Restoration Modes of Open-pit Coal Mine.},
journal = {Environmental management},
volume = {76},
number = {7},
pages = {},
pmid = {42400857},
issn = {1432-1009},
support = {HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; HNMYKJ20-08//Project of Science and Technology from China Huaneng Group Co., LTD/ ; },
mesh = {*Soil Microbiology ; *Rhizosphere ; *Soil/chemistry ; *Coal Mining ; Nitrogen/analysis ; *Microbiota ; Bacteria ; *Environmental Restoration and Remediation/methods ; Carbon/analysis ; },
abstract = {Microbial communities serve as vital indicators of ecosystem health and play a crucial role in facilitating the restoration of degraded soil ecosystems, acting as key participants in soil nutrient cycling. However, the interaction mechanisms between microbial communities and plants in different soil zones under varying restoration approaches remain unclear. This study focused on a restoration area of a decommissioned open-pit coal mine in an alpine region, comparing the microbial community structure and nutrient characteristics of rhizosphere and bulk soils under two restoration methods: herbaceous vegetation restoration and sea-buckthorn shrub restoration. The aim is to reveal the impact of different restoration measures on the soil-microorganism interactions. The results demonstrated that soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN), total potassium (TK), and available potassium (AK) contents were significantly higher in the herbaceous restoration area (O) than in the seabuckthorn area (S), by 51.7%, 88.6%, 38.2%, 13.1%, and 4.7%, respectively. Compared to bulk soil, rhizosphere soil exhibited higher microbial community diversity and richness. Furthermore, seabuckthorn rhizosphere microbial diversity surpassed that of herbaceous rhizosphere. Different restoration areas (DRE) significantly (p < 0.05) influenced the relative abundances of Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. The seabuckthorn area showed higher proportions of Proteobacteria (26.48 - 42.86%) and Actinobacteria (28.26 - 45.19%) compared to the herbaceous area. Functional gene prediction revealed that the seabuckthorn area expressed significantly higher abundances of core metabolic functional genes related to energy production and conversion (C), amino acid transport and metabolism (E), carbohydrate metabolism (G), and lipid metabolism (I) than the herbaceous area. Additionally, a symbiotic functional guild comprising animal pathogens, endophytes, lichen parasites, plant pathogens, and wood saprotrophs was formed in the seabuckthorn area. Redundancy analysis (RDA) indicated significant positive correlations (p < 0.05) between Acidobacteria, Chloroflexi, Actinobacteria, and Ascomycota and the contents of SOC, TN, and total phosphorus (TP). Bacterial networks formed with Actinobacteria as the core hub, comprising 300 edges connecting 50 nodes, while fungal networks were dominated by Ascomycota. Based on these findings, this study proposes a synergistic restoration strategy characterized by "herbaceous-induced short-term priming" coupled with "seabuckthorn-driven long-term stability." This strategy provides a theoretical foundation for the targeted microbial regulation of ecological restoration in mining areas.},
}

*Soil Microbiology
*Rhizosphere
*Soil/chemistry
*Coal Mining
Nitrogen/analysis
*Microbiota
Bacteria
*Environmental Restoration and Remediation/methods
Carbon/analysis

@article {pmid42404501,
year = {2026},
author = {Hossain, MJ and Mim, NA and Akter, N and Sony, SA and Saikat, EH and Hossain, MA and Parvin, N and Evan, MR and Juma, JJ and Roy, PP and Maruf, MFI and Islam, R and Labib, A and Shatabde, ZA and Das, M and Amanulla, M},
title = {Epidemiological Trends, Public Health Challenges, and Strategic Control Priorities of Dengue in Bangladesh (2000-2024): A Narrative Review.},
journal = {Health science reports},
volume = {9},
number = {7},
pages = {e72747},
pmid = {42404501},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Dengue has evolved into a major public health crisis in Bangladesh, transitioning from sporadic outbreaks to endemic transmission with increasing frequency and severity. The unprecedented 2023 epidemic recorded more deaths than the cumulative total of the previous two decades, highlighting the urgent need for a comprehensive synthesis of epidemiological trends and control challenges.

METHODS: This narrative review synthesizes published literature, surveillance reports, and national health data from 2000 to 2024 to examine the evolving epidemiology, clinical characteristics, transmission dynamics, and public health responses related to dengue in Bangladesh.

RESULTS: Epidemiological analysis reveals a dramatic rise in incidence and mortality, with widespread geographic expansion beyond Dhaka into southern and rural districts and a shift toward earlier seasonal peaks. Serotype transitions, particularly the dominance of DENV-3 followed by DENV-2-likely intensified disease severity through secondary infections. High case fatality rates were observed among females and older adults, with a substantial proportion of deaths occurring within 24 h of hospitalization, suggesting critical gaps in care-seeking and clinical management. Transmission dynamics are shaped by interactions between Aedes vector ecology, climate change, rapid urbanization, human mobility, and extensive insecticide resistance to pyrethroids. Public health responses remain constrained by passive surveillance, limited vector control efficacy, healthcare system strain, and insufficient community engagement.

CONCLUSIONS: The dengue burden of Bangladesh underscores the need for integrated and adaptive control strategies. Strengthening multi-domain surveillance (epidemiological, entomological, genomic), implementing resistance-aware Integrated Vector Management incorporating novel approaches such as Wolbachia, enhancing healthcare readiness, promoting community-driven behavioral interventions, integrating climate adaptation measures, and advancing vaccine and therapeutic research within a One Health framework are critical for sustainable dengue prevention and control.},
}

@article {pmid42406780,
year = {2026},
author = {Colombo, EH and Tarnita, CE and Bonachela, JA},
title = {Zooplankton feeding behavioral signatures in the morphology of macroscale prey spatial distribution.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014411},
pmid = {42406780},
issn = {1553-7358},
mesh = {Animals ; *Zooplankton/physiology ; *Feeding Behavior/physiology ; *Models, Biological ; *Predatory Behavior/physiology ; Ecosystem ; Food Chain ; Computational Biology ; Phytoplankton/physiology ; },
abstract = {The problem of pattern and scale remains central in ecology, bridging fundamental and applied questions. Marine microbial communities are a case in point. For instance, to understand the role of zooplankton in oceanic biogeochemistry, their response to changes in environmental conditions, and the implications for ecosystem services (e.g., fisheries), it is critical to understand zooplankton trophic interactions and how they change in a rapidly changing climate. This understanding, however, remains elusive because, unlike for phytoplankton, for which remote sensing of macroscale patterns can provide insight into their microscale dynamics and community composition, obtaining this information for zooplankton largely rests on quantifying the difficult-to-monitor microscale interactions among millions of individuals with different behaviors, and between individuals and their environment. Here, we investigate whether it is possible to obtain indirect information on zooplankton from the macroscale spatial distribution of their prey. To tackle this "problem of scale," we develop a rigorous coarse-graining methodology that connects individual-level properties with macroscale spatial patterns. We demonstrate that the shape of the prey spatial distribution can encode information about zooplankton feeding behavior and community dynamics. Specifically, we predict a change in dominant feeding behavior-from non-motile to motile feeding-as one moves from areas of high to areas of low prey density. These computational results are validated by our analysis of satellite images of oceanic blooms around the globe, which suggests novel opportunities for remote sensing approaches: the potential tracking of consumer behavioral signatures in the large-scale patterns of the resource. Importantly, the scaling-up methodology developed here to check for those signatures is general, and can be used to link scales rigorously and systematically in any system in which the complexity of individual dynamics makes connecting scales intractable.},
}

Animals
*Zooplankton/physiology
*Feeding Behavior/physiology
*Models, Biological
*Predatory Behavior/physiology
Ecosystem
Food Chain
Computational Biology
Phytoplankton/physiology

@article {pmid42407401,
year = {2026},
author = {Ibrahim, NA and Mehta, H and Sulieman, AME and Mir, RH and Fatima, SB and Adnan, M and Surti, M},
title = {Trichoderma-mediated biogenic synthesis of metal nanoparticles: Implications for soil health, plant resilience, and sustainable agroecosystems.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128614},
doi = {10.1016/j.micres.2026.128614},
pmid = {42407401},
issn = {1618-0623},
mesh = {*Trichoderma/metabolism ; *Metal Nanoparticles/chemistry ; Plant Development ; Soil Microbiology ; Agriculture/methods ; Agroecology ; Green Chemistry Technology ; Antifungal Agents/pharmacology ; Soil/chemistry ; Plants/microbiology ; Agrochemicals ; },
abstract = {The growing demand for sustainable agricultural practices has accelerated interest in eco-friendly alternatives to conventional agrochemicals. Among these, metal nanoparticles synthesized through biological routes have emerged as promising tools for crop protection and productivity enhancement. Trichoderma species, widely recognized for their biocontrol and plant growth-promoting properties, have gained considerable attention as efficient biofactories for the green synthesis of metal nanoparticles. The diverse metabolites produced by these fungi facilitate the reduction and stabilization of metal ions, resulting in nanoparticles with desirable physicochemical and biological properties. This review provides a comprehensive overview of the biosynthesis of metal nanoparticles by Trichoderma species, highlighting the underlying mechanisms, adaptation strategies to metal stress, and key physicochemical and biological factors influencing nanoparticle formation. Furthermore, the major types of Trichoderma-derived metal nanoparticles and their roles in antibacterial and antifungal activities, as well as plant growth promotion, are discussed. The potential of these nanoparticles to enhance plant health and support sustainable agricultural practices while minimizing the use of synthetic agrochemicals is also examined. Current limitations, challenges associated with field-level applications, and future research directions required for the successful translation of laboratory findings into practical agricultural systems are also discussed. Overall, Trichoderma-mediated nanoparticles represent a promising and sustainable approach for advancing next-generation agricultural technologies.},
}

*Trichoderma/metabolism
*Metal Nanoparticles/chemistry
Plant Development
Soil Microbiology
Agriculture/methods
Agroecology
Green Chemistry Technology
Antifungal Agents/pharmacology
Soil/chemistry
Plants/microbiology
Agrochemicals

@article {pmid42417989,
year = {2026},
author = {Castner, MD and Kitchen, C and Xiong, C and Bittle, MJ and Nestadt, PS and Wilcox, HC and Kharrazi, H},
title = {Assessing the utility of health access data and social determinants of health in ecological suicide prediction models.},
journal = {Social psychiatry and psychiatric epidemiology},
volume = {},
number = {},
pages = {},
pmid = {42417989},
issn = {1433-9285},
support = {R01 MH124724/MH/NIMH NIH HHS/United States ; R56 MH117560/MH/NIMH NIH HHS/United States ; R01 MH124724/MH/NIMH NIH HHS/United States ; },
abstract = {PURPOSE: Assess the utility of access to healthcare, clinical conditions, and social determinants of health (SDoH) variables in population-level suicide prediction models.

METHODS: Negative binomial regression models were constructed using data from population-level surveys, state death certificates, federal records of behavioral health services, and U.S. Census data. Outcomes of interest were suicidal ideation and suicide attempt (SISA), inpatient psychiatric hospitalization (IPH), and suicide death. The relative changes in pseudo R[2] were used to assess the impact of variable categories (i.e., clinical conditions, access to healthcare, and geo-derived SDoH) when added to a demographic-only baseline suicide prediction model.

RESULTS: Clinical data showed a significant impact, with the largest percent increase in pseudo R[2] compared to the demographic-only baseline model (321.9% for SISA; 736.9% for IPH; 18.9% for suicide death). Access to healthcare and geo-derived SDoH also improved model performances for all outcomes, but considerably lower than clinical variables. Models with all variable categories had the highest pseudo R[2], with .68, .58, and .46 for SISA, IPH, and suicide, respectively. Availability of emergency mental health services was found to be protective against IPH (IRR .90; 95% CI .84-.96) and suicide death (IRR .91; 95% CI .84-.97).

CONCLUSIONS: Clinical data proved to have the most effective variables in predicting a continuum of suicidal behaviors. While the impacts of access to healthcare and SDoH factors were comparatively limited, these variables also contributed to additional model improvements. These findings show the utility of population-level healthcare services and SDoH for ecological suicide behavior risk prediction.},
}

@article {pmid42390742,
year = {2026},
author = {Wu, S and Tatsis, EC},
title = {In Silico Identification and Comparative Synteny of Biosynthetic Gene Clusters in Plants.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {15-27},
pmid = {42390742},
issn = {1940-6029},
mesh = {*Multigene Family ; *Synteny ; *Computational Biology/methods ; *Plants/genetics/metabolism ; Software ; *Biosynthetic Pathways/genetics ; Genomics/methods ; Genome, Plant ; Computer Simulation ; Molecular Sequence Annotation ; },
abstract = {Biosynthetic gene clusters (BGCs) are often encoding specialized metabolic pathways in plants, yet effective methods for the comparison across multiple species are still evolving. In this protocol, we present a bioinformatics approach combining plantiSMASH and MCScan for the identification, annotation, and comparative analysis of BGCs in plant genomes. The methodology involves using plantiSMASH to predict and annotate potential BGCs, followed by the use of MCScan to perform syntenic analysis, enabling the exploration of the conservation and evolutionary dynamics of BGCs across different plant species. Here, we provide a step-by-step guide for installing and configuring the necessary software, preparing genomic data, and executing the analysis. This methodology, integrated with transcriptomic and metabolomic data, can be used to verify the functional relevance of the identified BGCs in specific biosynthetic pathways. It is applicable to a broad range of plant species and serves as a framework for the discovery and characterization of BGCs. The described methodology can significantly enhance research in plant genomics and metabolic engineering by offering new insights into the organization and function of BGCs.},
}

*Multigene Family
*Synteny
*Computational Biology/methods
*Plants/genetics/metabolism
Software
*Biosynthetic Pathways/genetics
Genomics/methods
Genome, Plant
Computer Simulation
Molecular Sequence Annotation

@article {pmid42391637,
year = {2026},
author = {Cui, B and van Beijnum, BJ and Tabak, M and Wang, Y},
title = {Sensor-Based Monitoring of Knee Osteoarthritis Symptoms in Free-Living Settings: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e84262},
pmid = {42391637},
issn = {1438-8871},
mesh = {Humans ; Digital Health ; Monitoring, Physiologic/instrumentation ; *Osteoarthritis, Knee/physiopathology/diagnosis ; Quality of Life ; *Wearable Electronic Devices ; },
abstract = {BACKGROUND: Knee osteoarthritis is a heterogeneous condition characterized by chronic pain, stiffness, and fatigue that fluctuate rapidly over time. Traditional clinical assessments provide only static diagnoses of disease severity, failing to capture the dynamic, day-to-day symptom variability that impacts patient quality of life. While wearable technologies offer the potential for continuous, high-frequency monitoring, previous reviews have examined general technological interventions for knee osteoarthritis management, yet they lack a specific synthesis of technologies for symptom monitoring.

OBJECTIVE: This study aims to synthesize current research on sensor technologies used for the continuous monitoring of knee osteoarthritis symptoms in free-living or simulated daily environments. Specifically, the review seeks to (1) map sensor modalities to specific symptom domains (biomechanical, physiological, and behavioral); (2) evaluate the alignment between objective sensor metrics and patient-reported outcome measures; and (3) identify gaps in current monitoring paradigms.

METHODS: A systematic literature search was conducted across PubMed, Embase, Web of Science, and IEEE Xplore. The review followed the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines. Eligibility criteria included studies involving participants with knee osteoarthritis using wearable or portable sensors capable of continuous monitoring (eg, inertial measurement units and electrocardiography) and assessing clinical symptoms (eg, pain, fatigue, and stiffness). Studies relying solely on stationary laboratory equipment (eg, force plates) without a portable component were excluded to ensure relevance to real-world applicability. Data regarding sensor types, sampling frequencies, monitored symptoms, and the statistical association between objective features and subjective symptom severity (key findings) were extracted.

RESULTS: A total of 16 studies met the inclusion criteria. The summary constructed from the results revealed a distinct technological saturation: the majority of studies (n=6) used inertial measurement units to quantify biomechanical deficits (eg, gait asymmetry and range of motion), which showed robust correlations with functional limitations. In contrast, there was a notable scarcity of research using physiological sensors (eg, electrocardiography and bioimpedance) to monitor systemic symptoms. Crucially, findings highlighted a significant discrepancy between subjective and objective data, particularly in sleep monitoring, where poor self-reported sleep quality predicted pain exacerbations despite stable objective actigraphy metrics. Furthermore, most systems operated as passive data loggers, with a lack of integration into active feedback loops.

CONCLUSIONS: Unlike previous reviews focused solely on biomechanics, this study innovatively maps the use of sensors across a multidimensional symptom spectrum, revealing a critical gap in the monitoring of fatigue and physiological stress. The findings suggest that current sensor applications are limited by a lack of integration with subjective patient experiences. Real-world implementation requires a hybrid monitoring paradigm that combines the ecological validity of wearable sensors with the clinical relevance of patient-reported outcomes. This approach paves the way for digital phenotyping and active feedback systems, offering a personalized strategy for managing the complex symptom burden of knee osteoarthritis.},
}

Humans
Digital Health
Monitoring, Physiologic/instrumentation
*Osteoarthritis, Knee/physiopathology/diagnosis
Quality of Life
*Wearable Electronic Devices

@article {pmid42391685,
year = {2026},
author = {Hirose, K and Inomata, Y and Povinec, PP and Tsumune, D and Yamada, M and Zheng, J},
title = {Temporal trends and tracing capabilities of plutonium in the western North Pacific Ocean.},
journal = {Journal of environmental radioactivity},
volume = {298},
number = {},
pages = {108086},
doi = {10.1016/j.jenvrad.2026.108086},
pmid = {42391685},
issn = {1879-1700},
abstract = {Plutonium is a valuable temporal and spatial tracer in biogeochemical research due to its strong chemical reactivity, serving as a significant resource for tracking water mass movement. Because two major sources of plutonium exist in the North Pacific Ocean - global fallout (GF-Pu) from nuclear weapons tests and close-in fallout from the US Pacific Proving Ground (PPG-Pu), investigating its distribution and cycling is highly viable. Here, we examine temporal and spatial changes in [239,240]Pu activity concentrations and [240]Pu/[239]Pu atom ratios in surface and deep waters by analyzing Pu data from 1960 to 2020. Surface [239,240]Pu in the subarctic North Pacific has showed a declining trend after 2000, with a rate of decrease comparable to that in the subtropical region (apparent half-life of 6.4 y). Deep [239,240]Pu levels in the North Pacific also declined on a decadal timescale, likely reflecting the northward flow of deep water with low [239,240]Pu concentrations near 20°N. The [240]Pu/[239]Pu atom ratio in surface waters of the subtropical North Pacific indicates that GF-derived Pu ([240]Pu/[239]Pu atom ratio of 0.18) dominated surface Pu levels until 1980, after which PPG-derived Pu ([240]Pu/[239]Pu atom ratio of 0.33) became the dominant component. In the deep waters of the North Pacific, PPG-Pu signals were detected in the subarctic region during 1981 and 1988. Consequently, the [240]Pu/[239]Pu atom ratio serves as a powerful tool for unraveling the complexities of Pu cycling. These observations are important for better understanding of surface and deep-water flows, vertical motion, and biogeochemical processes in the western North Pacific Ocean.},
}

@article {pmid42392792,
year = {2026},
author = {Abbà, S and Vallino, M and Cicerone, A and Cirrincione, S and Aiuto, B and Galetto, L and Rossi, M},
title = {Multi-Omics Profiling of the Scaphoideus titanus Yeast-Like Symbiont Guides the Bioinformatic Discovery of Related Fungal Symbioses in Insects.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70361},
pmid = {42392792},
issn = {1462-2920},
support = {CUP B17G23000320005//Ministero dell'Agricoltura, della Sovranità Alimentare e delle Foreste; Project MICOTI/ ; },
mesh = {Animals ; *Symbiosis ; *Hemiptera/microbiology ; Phylogeny ; Computational Biology ; Multiomics ; Proteomics ; *Hypocreales/genetics/classification ; Genomics ; },
abstract = {Symbiotic partnerships have opened new ecological niches and contributed to the remarkable diversification of insects. The leafhopper Scaphoideus titanus, a phloem-feeding insect known to be the primary vector of Flavescence dorée phytoplasma, harbours two primary endosymbionts: the bacterium 'Candidatus Karelsulcia muelleri' and a yeast-like symbiont (YLS). While most studies on insect-associated microorganisms have focused on obligate bacterial symbionts, fungal endosymbionts, although documented for almost a century, are only now gaining renewed attention for their evolutionary and ecological significance. In this study, we integrated genomic and proteomic data with phylogenetic analyses to elucidate the functional and evolutionary features of the YLS associated with S. titanus. Using a data-independent proteomic approach supported by a newly sequenced symbiont genome, we defined the proteins expressed by the YLS that may contribute to host physiology. Comparative analyses across the five currently available YLS genomes enabled a proteome-wide phylogenetic reconstruction within the genus Ophiocordyceps, refining the evolutionary placement of these symbioses. Finally, large-scale mining of NCBI transcriptomic Sequence Read Archive datasets using a novel computational workflow, combined with an extensive literature survey, identified several new candidate insect hosts and provided a comprehensive inventory of species harbouring these fungal partners.},
}

Animals
*Symbiosis
*Hemiptera/microbiology
Phylogeny
Computational Biology
Multiomics
Proteomics
*Hypocreales/genetics/classification
Genomics

@article {pmid41604136,
year = {2026},
author = {Qian, Z and Tian, J and Chen, Q and Zhang, Y and Zhang, C and Yin, S and Zhang, K},
title = {Multi-Omics Analysis Uncovers Acute Hypoxia-Induced Gut Damage and the Underlying Protective Mechanisms of Probiotic Clostridium butyricum B3 in Yellow Catfish (Pelteobagrus fulvidraco).},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {5},
pages = {6945-6964},
pmid = {41604136},
issn = {1867-1314},
support = {JBGS[2021]034//The "JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; 32102760//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Catfishes/microbiology/metabolism ; *Probiotics/administration & dosage/pharmacology ; *Clostridium butyricum/physiology ; Multiomics ; *Hypoxia/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Acute hypoxia stress poses a significant challenge in aquaculture, not only compromising gut health but also resulting in substantial economic losses. Using an integrated multi-omics approach, this study demonstrates that hypoxia severely disrupts the intestinal function of yellow catfish (Pelteobagrus fulvidraco), specifically manifesting as phospholipid metabolism disorders, inhibited fatty acid β-oxidation, reduced short-chain fatty acid (SCFA) synthesis, imbalanced gut microbiota (e.g., decreased levels of beneficial lactic acid bacteria Lactococcus and Clostridium sensu stricto 1), and downregulation of detoxification pathways mediated by cytochrome P450. Building upon the previously isolated and identified high-yield SCFA-producing probiotic Clostridium butyricum B3 from yellow catfish in early work, this research further investigated the efficacy and mechanisms of B3 supplementation in mitigating hypoxia-induced intestinal barrier damage in yellow catfish. The results indicated that the supplementation of C. butyricum B3, particularly at a dose of 3.0 × 10[7] CFU/g, significantly reduced histological damage, enhanced the expression of key tight junction proteins (such as ZO-1 and Claudin), and modulated hypoxia-inducible factor signaling pathways (including HIF-1α, FIH, and PHD). Furthermore, the application of C. butyricum B3 restored microbial ecological balance by promoting the growth of beneficial bacteria like Cetobacterium and inhibiting potential pathogens such as Acinetobacter. In conclusion, these findings underscore the potential of C. butyricum B3 as a novel probiotic strategy for enhancing fish hypoxia tolerance and maintaining intestinal integrity, offering valuable insights for sustainable aquaculture practices.},
}

Animals
*Catfishes/microbiology/metabolism
*Probiotics/administration & dosage/pharmacology
*Clostridium butyricum/physiology
Multiomics
*Hypoxia/metabolism
Gastrointestinal Microbiome/drug effects

@article {pmid42283564,
year = {2026},
author = {Ardizzone, CM and Lammons, JW and Lan, RS and Elnaggar, JH and Lillis, RA and Toh, E and Pack, LM and Mott, PD and Jacobs, CD and Yeruva, L and Taylor, CM and Quayle, AJ},
title = {Integrated multi-omics analysis uncovers cervicovaginal ecological networks and their association with Chlamydia trachomatis load.},
journal = {Infection and immunity},
volume = {94},
number = {7},
pages = {e0068125},
doi = {10.1128/iai.00681-25},
pmid = {42283564},
issn = {1098-5522},
support = {T32 AI060519/NH/NIH HHS/United States ; R01 AI118860/NH/NIH HHS/United States ; },
mesh = {Female ; Humans ; Multiomics ; *Chlamydia trachomatis/physiology ; *Vagina/microbiology ; *Chlamydia Infections/microbiology ; Cytokines/metabolism ; Microbiota ; Vaginosis, Bacterial/microbiology ; Tryptophan/metabolism ; *Cervix Uteri/microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; *Bacterial Load ; Tandem Mass Spectrometry ; },
abstract = {Chlamydia trachomatis (Ct) is a causal agent of upper reproductive tract pathology. There is a broad spectrum of cervical Ct load in infected women, and upper tract infection is associated with higher cervical Ct load. Recent studies indicate that bacterial vaginosis (BV) can modulate host-Ct outcomes. To identify features associated with BV status and Ct load, we performed an integrated multi-omics analysis of the cervicovaginal microbiome, tryptophan metabolome, and cytokines. Samples were analyzed using 16S rRNA gene sequencing, targeted UPLC-MS/MS quantification of tryptophan metabolites, and multiplex cytokine profiling. Ordination analyses showed that BV status was separated by the microbiome, metabolome, and cytokines, whereas Ct load was separated only by cytokines. K-means clustering of tryptophan metabolites defined three metabolome state types (MSTs). MST I, associated primarily with Lactobacillus crispatus-dominated community state type (CST) I, exhibited high tryptophan availability, indole-3-lactic acid, and complete kynurenine-pathway activity. Both MST II and MST III were associated with BV-associated CST IV and showed marked tryptophan depletion. MST II was broadly depleted of most tryptophan metabolites, while MST III was enriched in downstream microbially derived indole pathway metabolites and kynurenic acid. Hierarchical all-against-all association testing revealed coordinated relationships linking clusters of bacterial taxa, metabolites, and cytokines. Importantly, multi-omics network analyses identified integrated microbial-metabolic-immune modules that predicted high versus low Ct load, highlighting CXCL9, CXCL10, IL-17, BV-associated taxa, and indole pathway metabolites as key discriminative features. Results demonstrate that cervical Ct load reflects coordinated microbial-metabolic-immune ecological states rather than microbiome composition alone and refine current models of Ct-BV interactions.},
}

Female
Humans
Multiomics
*Chlamydia trachomatis/physiology
*Vagina/microbiology
*Chlamydia Infections/microbiology
Cytokines/metabolism
Microbiota
Vaginosis, Bacterial/microbiology
Tryptophan/metabolism
*Cervix Uteri/microbiology
Metabolome
RNA, Ribosomal, 16S/genetics
*Bacterial Load
Tandem Mass Spectrometry

@article {pmid42374709,
year = {2026},
author = {Yuan, R and Shu, P and Salam, M and Wu, S and Liu, Y and Li, H and Li, W},
title = {Cadmium(II) Loading Exacerbates the Negative Effects of Nanobiochar on Daphnia magna: Evidence from Toxicity Test and Multiomics Analysis.},
journal = {Environmental science & technology},
volume = {60},
number = {27},
pages = {19090-19105},
doi = {10.1021/acs.est.6c01162},
pmid = {42374709},
issn = {1520-5851},
mesh = {Animals ; *Daphnia magna/drug effects ; *Cadmium ; Multiomics ; Water Pollutants, Chemical ; Toxicity Tests ; Daphnia ; Charcoal ; },
abstract = {Micro- (M-BC) and nanobiochar (N-BC) particles exhibit strong environmental mobility and superior adsorption capacity for heavy metals. This raises concerns regarding their ecological risks to aquatic ecosystems. However, systematic studies on the toxicity of contaminant-laden M-BC and N-BC to aquatic biota remain scarce. Here, we prepared the cadmium (Cd(II))-loaded complexes (M-BC-Cd and N-BC-Cd), identified the acute toxicity of M-BC-Cd and N-BC-Cd on zooplankton Daphnia magna, and emphasized the response in D. magna induced by N-BC and N-BC-Cd. The results indicated that N-BC alone induced minimal adverse effects on D. magna. N-BC demonstrated a higher Cd(II) adsorption capacity than M-BC, leading to a lower LC50 level for N-BC-Cd. In chronic toxicity tests, exposure to N-BC-Cd resulted in a 30% reduction in the survival of D. magna compared to that of N-BC. The particles of N-BC-Cd caused more severe impairment in growth, reproduction, and oxidative stress responses. While N-BC primarily affected predation efficiency and disrupted metabolic pathways, the amplified toxicity of N-BC-Cd was attributed to a synergistic effect of prey limitation, metabolic dysregulation, oxidative stress, inhibition of signal transduction, and down-regulation of lysosomal proteins. This finding provides novel insights into assessing the environmental risks of biochar particles in aquatic ecosystems.},
}

Animals
*Daphnia magna/drug effects
*Cadmium
Multiomics
Water Pollutants, Chemical
Toxicity Tests
Daphnia
Charcoal

@article {pmid42390619,
year = {2026},
author = {Ahlendorf, A and Aharoni, A and Vahabi, K and Fischer, TG and Allard, PM and Augustin, M and Bathe, U and Broadhurst, DI and Broeckling, C and Buescher, J and Covaci, A and da Silva, KM and de Vos, RCH and Devi, MG and Döll, S and Frey, M and Frolov, A and Gaquerel, E and Gautam, V and Charria-Girón, E and Goossens, A and Grosjean, J and Halabalaki, M and Iturrospe, E and Kultima, K and Herman, S and Kutchan, TM and Larbat, R and Meier, R and Mikropoulou, EV and Mouille, G and Nicolotti, L and Shahaf, N and Perreau, F and Pétriacq, P and Reichelt, M and Reinke, SN and Robeyns, R and Soboleva, A and Spring, O and Sreenivasan, AP and Tissier, A and Totozafy, JC and Tsugawa, H and Valls-Fonayet, J and van de Lavoir, M and van der Hooft, JJJ and Vergara, F and Wishart, D and Wessjohann, LA and Wolfender, JL and Ziegler, J and Balcke, GU and Neumann, S},
title = {The MassBank contributions of the mFam collaboration.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {4},
pages = {},
pmid = {42390619},
issn = {1573-3890},
mesh = {*Metabolomics/methods ; *Tandem Mass Spectrometry/methods ; Animals ; *Metabolome ; Databases, Factual ; Mass Spectrometry/methods ; },
abstract = {INTRODUCTION: The analysis of metabolic profiles using high resolution mass spectrometry (MS) data provides deep insights into biological processes. In metabolomics, MS analysis generates a large number of features that represent metabolites. However, identifying specific metabolites from these features can be challenging. One of the major bottlenecks in the metabolomics field is the identification of MS features, which is a prerequisite for any biochemical interpretation. By identifying similarities and differences within a metabolite family (mFam), evaluating MS features at the metabolite family level can help assigning functional roles to individual MS features. These data can help interpreting metabolic pathways and processes within a biological system. For the assignment of metabolite families to MS features, it is important to have good quality, reliable, and comprehensive spectral libraries.

OBJECTIVE: We initiated a global effort to collect high-resolution MS/MS spectra of metabolites from labs working in different fields, including metabolomics of animals, microorganisms, and plants. The mFam-MS/MS collection delivers valuable training data to assign machine-readable classified information on the unknown metabolites.

RESULTS: The mFam collaboration used a standardized metadata template and has developed a globally curated MS/MS spectral library of 7,872 spectra with 2,126 unique metabolites. This library was compiled from 47 datasets contributed by 25 laboratories measured on 12 instrument types, including QTOF, Orbitrap, and Ion Mobility-QTOF systems. It comprises 4,646 spectra in positive mode and 3,226 in negative mode. This standardized resource significantly enhances metabolite identification capabilities, supports the development of machine learning-based annotation tools, and accelerates the discovery of novel metabolites. All spectra are available under the collective contributor label mFam in the MassBank system, including the web interface and the 2025.10 data release available at GitHub and Zenodo.},
}

*Metabolomics/methods
*Tandem Mass Spectrometry/methods
Animals
*Metabolome
Databases, Factual
Mass Spectrometry/methods

@article {pmid42390741,
year = {2026},
author = {Konkel, Z and Slot, J},
title = {Generalized Gene Cluster Detection Using CLOCI.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3054},
number = {},
pages = {1-14},
pmid = {42390741},
issn = {1940-6029},
mesh = {*Multigene Family ; Algorithms ; *Genomics/methods ; *Software ; *Computational Biology/methods ; Evolution, Molecular ; Clustering Algorithms ; Synteny ; },
abstract = {Metabolic gene clusters (MGCs) are genomic loci that contain multiple genes that are functionally and genetically linked. MGCs collectively encode a spectrum of metabolic functions, including small molecule biosynthesis, nutrient assimilation, metabolite degradation, and production of proteins essential for growth and development. Due to their diverse ecological functions, identifying gene clusters is a powerful tool for small molecule discovery and provides insight into the ecology and evolution of organisms. Gene cluster detection algorithms have historically been specialized for detecting biosynthetic gene clusters that contain canonical "core" biosynthetic functions, while overlooking uncommon or unknown cluster classes. These overlooked clusters are a potential source of novel natural products and comprise an untold portion of overall gene cluster repertoires. Unbiased, function-agnostic detection algorithms therefore provide an opportunity to reveal novel classes of gene clusters and more precisely define genome organization.We developed CLOCI (Co-occurrence Locus and Orthologous Cluster Identifier) as a generalized, unbiased gene cluster detection algorithm. CLOCI generalizes gene cluster detection by identifying signatures of coordinated gene evolution that underlie all classes of MGCs. CLOCI first detects selection on gene colocalization by identifying and circumscribing shared synteny loci across a dataset of genomes into homologous locus groups. Gene clusters comprise a subset of these homologous locus groups, and CLOCI implements orthogonal proxies of coordinated gene evolution, such as quantifying loss and horizontal transfer of a locus, to enrich MGCs from homologous loci. Here, we describe the conceptual framework of the CLOCI algorithm and present a description of its implementation (see Note 1).},
}

*Multigene Family
Algorithms
*Genomics/methods
*Software
*Computational Biology/methods
Evolution, Molecular
Clustering Algorithms
Synteny

@article {pmid42330077,
year = {2026},
author = {Creus-Martí, I and Moya, A and Santonja, FJ},
title = {CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data.},
journal = {PLoS computational biology},
volume = {22},
number = {6},
pages = {e1014328},
doi = {10.1371/journal.pcbi.1014328},
pmid = {42330077},
issn = {1553-7358},
mesh = {*Microbiota/genetics/physiology ; *Software ; *Computational Biology/methods ; Bacteria/genetics/classification ; Animals ; Longitudinal Studies ; Humans ; Models, Biological ; },
abstract = {In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.},
}

*Microbiota/genetics/physiology
*Software
*Computational Biology/methods
Bacteria/genetics/classification
Animals
Longitudinal Studies
Humans
Models, Biological

@article {pmid42387942,
year = {2026},
author = {Saudreau, C and Tarazona, V and De Bandt, D},
title = {French Consumption of Methylphenidate in Primary Care From 2016 to 2023, Impact of Prescribing Policy Changes-A Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {35},
number = {7},
pages = {e70424},
pmid = {42387942},
issn = {1099-1557},
mesh = {*Methylphenidate/therapeutic use/economics/administration & dosage ; France ; Humans ; *Central Nervous System Stimulants/therapeutic use/economics/administration & dosage ; *Attention Deficit Disorder with Hyperactivity/drug therapy ; *Practice Patterns, Physicians'/trends/statistics & numerical data/economics ; *Primary Health Care/trends/statistics & numerical data/economics ; Drug Prescriptions/statistics & numerical data ; Health Policy ; Databases, Factual ; Drug Utilization/trends ; },
abstract = {PURPOSE: In France, methylphenidate, mainly used in the treatment of ADHD, has been subject to prescription restrictions that were relaxed at the end of 2021. This study analyses trends in methylphenidate consumption in France and examines changes following the modification to prescribing rules in 2021.

METHODS: This ecological study was based on data from the Medic'AM database, which records reimbursed outpatient drug dispensation in France from January 2016 to December 2023. Methylphenidate sales were expressed as defined daily dose per thousand inhabitants per day (DDD/TID) and expenditure as euros per thousand inhabitants. Time-series analyses were conducted to assess changes in methylphenidate sales and associated expenditure following modifications to prescribing arrangements in September and November 2021.

RESULTS: Methylphenidate consumption rose from 0.607 DDD/TID per month in 2016 to 1.457 DDD/TID in 2023, an increase of 84%. Associated expenditure followed a similar upward trend. A more pronounced increase in methylphenidate sales was observed after the end of 2021.

CONCLUSION: The study shows a clear increase in methylphenidate sales after 2021, coinciding with changes in prescribing regulations. Given the ecological design, this temporal association cannot be interpreted as causal. The observed trends likely reflect multiple factors, including regulatory changes, increased recognition of ADHD, and evolving clinical practices. These findings highlight how changes in prescribing policies may be associated with variation in healthcare utilization and expenditure.},
}

*Methylphenidate/therapeutic use/economics/administration & dosage
France
Humans
*Central Nervous System Stimulants/therapeutic use/economics/administration & dosage
*Attention Deficit Disorder with Hyperactivity/drug therapy
*Practice Patterns, Physicians'/trends/statistics & numerical data/economics
*Primary Health Care/trends/statistics & numerical data/economics
Drug Prescriptions/statistics & numerical data
Health Policy
Databases, Factual
Drug Utilization/trends

@article {pmid42389374,
year = {2026},
author = {Perea García, JO and Kano, F and Sibierska, M and Fiala, V and Skrok, MK and Danel, DP and Ratajczak, EK and Zywiczynski, P and Wacewicz, S},
title = {Gaze in context: non-human eyes can be more salient under ecologically relevant conditions.},
journal = {Evolutionary human sciences},
volume = {8},
number = {},
pages = {e25},
pmid = {42389374},
issn = {2513-843X},
abstract = {Primate eyes vary strikingly in pigmentation, yet the drivers of said variation are strongly debated. Recent revisions of the cooperative eye hypothesis propose that the human eye's sclera evolved to enhance gaze communication specifically under challenging conditions of visibility. We tested this idea under ecologically realistic conditions by presenting observers with a live model wearing contact lenses that simulated either a human-like or a chimpanzee-like eye. At a university lab, observers judged gaze direction at different viewing distances and lighting levels. We found no overall difference in efficacy of different eye types. Contrary to expectations, chimpanzee-like eyes outperformed human-like eyes in dim lighting and close-viewing conditions. Human-like eyes yielded the highest accuracy under bright, far-viewing conditions, consistent with a long-distance signalling advantage. Our results demonstrate that ecological visual constraints shape the potential informativeness of distinct ocular configurations. We hypothesize that species-typical eye appearances may be tuned to their species-typical visual ecology.},
}

@article {pmid42091894,
year = {2026},
author = {Solano, I and Bro-Jørgensen, J and Lazagabaster, IA and Thomas, CD and Manzano, S},
title = {NAMPHORA: a fossil and modern pollen database from Northern Africa and adjacent Mediterranean and Arabian regions.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42091894},
issn = {2052-4463},
support = {Grant: NE/S00713X/1//Adapting to the Challenges of a Changing Environment (ACCE) Doctoral Training Partnership, funded by the Natural Environment Research Council (NERC)/ ; Grant: RPG-2021-104//Biodiversity in Ancient Egypt during Societal Transitions (BEAST) project, funded by Leverhulme Trust/ ; Grant: RYC2021-034991-I//Ministerio de Ciencia e Innovación de España MCIN/AEI/10.13039/501100011033 and European Union NextGenerationEU/PRTR./ ; Grant: PID2024-161027NA-I00 DivAS-Cape//MICIU/AEI/ 10.13039/501100011033 and by the ERDF/EU/ ; },
mesh = {*Pollen ; *Fossils ; Africa, Northern ; Mediterranean Region ; Climate ; *Databases, Factual ; Plants ; },
abstract = {Northern Africa's climate and vegetation underwent significant changes throughout the Holocene, particularly in connection with the termination of the African Humid Period ca. 5500 years ago. Fossil pollen records are key to reconstructing past environments, yet current databases for this region are limited by the omission of significant unpublished data, taxonomic inconsistencies, and the lack of standardised plant trait information. To address these issues, we introduce the Northern African, Arabian, and Mediterranean Pollen Holocene Records Archive (NAMPHORA)- a comprehensive, machine-readable and taxonomically-harmonised database compiling fossil and modern pollen records alongside plant functional traits, and ecological and phytogeographical information. This database includes all of Africa to the north of 7.52° N and constitutes the most complete and comprehensive resource (836 pollen records; 853 harmonised pollen types, and 13 key standardised plant traits) to improve palaeoecological reconstructions, enhance biogeographical analyses, and refine climate models for northern Africa during the Holocene. It enables direct data retrieval via programming languages such as R, and all datasets and code are openly available via Zenodo.},
}

*Pollen
*Fossils
Africa, Northern
Mediterranean Region
Climate
*Databases, Factual
Plants

@article {pmid42387317,
year = {2026},
author = {Chen, Z and Wang, S and Sun, Z and Liao, H and Longji, Y and Zhang, Q and Wang, J},
title = {An AI-Driven Multi-Omics Framework Identifies CASP8 as a Clinically Actionable Pyroptosis Biomarker in Bladder Cancer.},
journal = {BioFactors (Oxford, England)},
volume = {52},
number = {4},
pages = {e70130},
doi = {10.1002/biof.70130},
pmid = {42387317},
issn = {1872-8081},
mesh = {*Urinary Bladder Neoplasms/genetics/pathology/metabolism ; Humans ; *Biomarkers, Tumor/genetics/metabolism ; *Caspase 8/genetics/metabolism ; *Pyroptosis/genetics ; Machine Learning ; Multiomics ; Gene Expression Regulation, Neoplastic ; Cell Line, Tumor ; Tumor Microenvironment/genetics ; Genomic Instability ; Artificial Intelligence ; },
abstract = {Despite rapid advances in multi-omics technologies, translating candidate biomarkers into clinical practice for bladder cancer remains challenging due to the difficulty of linking complex genomic instability to interpretable biological processes. To address this, we developed an AI-driven multi-omics discovery framework integrating single-cell RNA sequencing, multi-cohort transcriptomics, and machine learning-based genomic inference. By analyzing chromosomal aneuploidy and copy number variations at single-cell resolution, we identified malignant cell populations and constructed a consensus pyroptosis scoring system, followed by machine learning-assisted biomarker screening and experimental validation. Our results reveal that while global pyroptosis activity is elevated in the bladder cancer microenvironment, malignant cells with high genomic instability exhibit significant pyroptosis suppression. Through this pipeline, CASP8 was identified as a key clinically relevant biomarker; its low expression correlates strongly with increased tumor mutation burden, frequent driver gene alterations (including TP53 and RB1), and poor survival outcomes. Functional assays further confirmed that CASP8 loss promotes malignant phenotypes and alters cell death programs. Ultimately, this study establishes a next-generation framework for biomarker translation, highlighting CASP8 as a clinically actionable link between genomic instability and pyroptosis dysregulation, and demonstrating the power of AI-integrated strategies in accelerating bladder cancer research from bench to bedside.},
}

*Urinary Bladder Neoplasms/genetics/pathology/metabolism
Humans
*Biomarkers, Tumor/genetics/metabolism
*Caspase 8/genetics/metabolism
*Pyroptosis/genetics
Machine Learning
Multiomics
Gene Expression Regulation, Neoplastic
Cell Line, Tumor
Tumor Microenvironment/genetics
Genomic Instability
Artificial Intelligence

@article {pmid42275736,
year = {2026},
author = {Barcan, RA and Carradori, S and Samsing, F and Nguyen, NL and He, L and Wang, Y and Barcan, AS},
title = {Machine learning in applied microbiology, from data quality to model validation and implementation.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128588},
doi = {10.1016/j.micres.2026.128588},
pmid = {42275736},
issn = {1618-0623},
mesh = {*Machine Learning ; *Microbiology ; Reproducibility of Results ; Microbiota ; Classification Algorithms ; Predictive Learning Models ; Humans ; Databases, Factual ; },
abstract = {Machine learning (ML) is now widely applied in microbiology, but its reliability varies markedly across domains. In this review, we analysed data from 254 scientific articles that evaluates ML through three linked dimensions including data readiness, model suitability, and deployment readiness across diagnostics and pathogen identification, virology, microbiome research, industrial and environmental microbial biotechnology. This framework helps distinguish robust progress from performance inflated by methodological limitations. Our review shows that pathogen identification and antimicrobial resistance prediction consistently achieve strong performance when supported by curated datasets, reliable labels, and comprehensive reference databases. However, their practical value remains limited by internal validation, lineage confounding, and uneven transfer across strains, institutions, and regions. In virological studies, predictive stability is further challenged by incomplete reference databases, changing taxonomy, and temporal drift during outbreaks. In microbiome research, ML classifiers can detect disease and environmental signals, but their generalization across cohorts remains weak because of compositional data structure, technical bias, and incomplete metadata. Industrial bioprocessing and environmental applications show promise when process data are rich and controlled, but deployment beyond laboratory or site-specific settings remains limited. Across structured microbiological datasets, classical supervised models often remain competitive with deep learning while being easier to interpret and validate. Detailed quantitative benchmarks supporting these comparisons are synthesized in the main text and summary tables. Overall, progress will depend less on algorithmic novelty than on interoperable and well-annotated datasets, representative sampling, standardized benchmarking, reproducible workflows, and prospective multi-site validation.},
}

*Machine Learning
*Microbiology
Reproducibility of Results
Microbiota
Classification Algorithms
Predictive Learning Models
Humans
Databases, Factual

@article {pmid42321367,
year = {2026},
author = {Wang, X and Zhang, C and Wang, H and Reid, K and Merilä, J},
title = {How precise are mutation rate estimates? Comparison of different approaches to estimate de novo mutation rates.},
journal = {Heredity},
volume = {135},
number = {6},
pages = {445-452},
pmid = {42321367},
issn = {1365-2540},
support = {202111159018//University Grants Committee (UGC)/ ; },
mesh = {Animals ; *Mutation Rate ; *Computational Biology/methods ; Sequence Analysis, DNA ; Mutation ; High-Throughput Nucleotide Sequencing ; },
abstract = {Availability of de novo mutation rate (µ) estimates based on approaches that rely on bioinformatic validations has increased tremendously during the past few years, but the accuracy and precision of these estimates often remain unclear as Sanger sequencing validation of the mutations is often lacking. We used both long- and short-read sequencing data and different bioinformatic pipelines to estimate µ, as well as false positive (FPR) and negative (FNR) rates, for family trios of flat-headed loaches (Oreonectes platycephalus). By comparing estimates against PCR-verified mutations, we observed that the top-performing approach (as ranked by the F1 score of seven approaches at the same depth) still exhibited a 4% false positive rate (FPR) alongside a 12% false-negative rate (FNR). Across the remaining methods, FPR values ranged from 4-12%, and FNRs from 8-19%. Irrespective of the bioinformatic approach used, long-read data yielded consistently lower µ estimates than short-read data because of the larger callable genome sizes. In addition, a higher mapping depth resulted in a lower FNR. These results call for caution regarding de novo mutations without Sanger sequencing validation in non-model organisms and raise the possibility that many published µ-estimates, especially those based on low mapping depths, might be biased.},
}

Animals
*Mutation Rate
*Computational Biology/methods
Sequence Analysis, DNA
Mutation
High-Throughput Nucleotide Sequencing