@article {pmid41538056,
year = {2026},
author = {Rehman, U and Sarfraz, M and Bibi, F and Noor, A and Ullah, M and Tarafder, E and Shinwari, ZK},
title = {DNA barcoding and phylogenomics in mushrooms: current progress, challenges, and future prospects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {2},
pages = {40},
pmid = {41538056},
issn = {1572-9699},
mesh = {*DNA Barcoding, Taxonomic/methods/trends ; *Agaricales/genetics/classification ; Multiomics ; *Phylogeny ; Genomics/methods ; Genome, Fungal ; High-Throughput Nucleotide Sequencing ; },
abstract = {Mushrooms represent a taxonomically and ecologically diverse group of fungi with profound significance for ecosystems, biotechnology, and human welfare. However, their accurate identification and classification have long been hindered by morphological convergence, cryptic speciation, and limited diagnostic traits. This review synthesizes recent progress in DNA barcoding, phylogenomics, and multi-omics approaches that are reshaping the molecular systematics of mushrooms. The internal transcribed spacer (ITS) region remains the universal fungal barcode, yet its limitations have driven the adoption of multilocus and genome-scale datasets for deeper evolutionary resolution. Advances in high-throughput sequencing (HTS), whole-genome phylogenies, and core-gene frameworks have refined species boundaries and clarified evolutionary trajectories across major fungal lineages. The integration of multi-omics platforms including genomics, transcriptomics, proteomics, and metabolomics has enabled holistic insights into fungal metabolism, adaptation, and ecological functions. Despite these advances, challenges persist, including database inconsistencies, incomplete sampling, and analytical complexities. Addressing these issues through standardized molecular protocols, AI-driven data analytics, and global open-data collaboration will be essential for achieving reproducible and evolutionarily coherent fungal systematics. Ultimately, the convergence of barcoding, phylogenomics, and omics technologies represents a transformative step toward an integrative, data-driven framework for understanding and utilizing fungal diversity in science, sustainability, and innovation.},
}

*DNA Barcoding, Taxonomic/methods/trends
*Agaricales/genetics/classification
Multiomics
*Phylogeny
Genomics/methods
Genome, Fungal
High-Throughput Nucleotide Sequencing

@article {pmid41538613,
year = {2025},
author = {Soares Filho, AM and Vasconcelos, CH and Vasconcelos, NM and Lima, CM and Souza, MFM and Pinto, IV and Cardoso, LO and Malta, DC},
title = {Mapping of underreporting of interpersonal violence based on the occurrence of homicides in Brazilian municipalities, 2016-2018.},
journal = {Ciencia & saude coletiva},
volume = {30},
number = {12},
pages = {e08432024},
doi = {10.1590/1413-812320253012.08432024},
pmid = {41538613},
issn = {1678-4561},
mesh = {Brazil/epidemiology ; Humans ; *Homicide/statistics & numerical data ; Female ; *Violence/statistics & numerical data ; Adult ; Cities ; Middle Aged ; Young Adult ; *Information Systems/statistics & numerical data ; },
abstract = {Identify municipalities with underreporting of interpersonal violence based on homicide in Brazil, 2016 to 2018. Ecological study with rate on violence from the Notifiable Diseases Information System and homicide estimates from the Global Burden of Disease concerning < 20 years, women of 20 to 59 years, ≥ 60 years and the total of these subgroups. Bivariate Local Moran identified clusters of critical areas of low reporting rates and high homicide rates (p < 0.05). Municipalities in the North, Northeast, and Midwest of Brazil represented 29% of all reports of violence and 58% of homicides. The majority of these municipalities were concentrated in low reporting rates (≤ 0.8/10,000) and high homicide rates (≥ 13.7/100,000); and 31.4% of municipalities with high homicide rate reported zero cases. Reports of violence and homicide rates showed a negative spatial correlation (I<20 = -0.083; Iwomen20-59 = -0.023; I≥60 = -0.086; Itotal = -0.085), showing that nearby places have inverse values. Critical municipalities for underreporting of violence reach 16% of < 20 years, 12% of women, 23% of the elderly, and 18% in total. The low reporting in seriously violent areas provides evidence of underreporting. The findings can provide management with tools for initiatives to improve violence surveillance and access to the protection network.},
}

Brazil/epidemiology
Humans
*Homicide/statistics & numerical data
Female
*Violence/statistics & numerical data
Adult
Cities
Middle Aged
Young Adult
*Information Systems/statistics & numerical data

@article {pmid42166940,
year = {2026},
author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM},
title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.},
journal = {Pathology, research and practice},
volume = {285},
number = {},
pages = {156543},
doi = {10.1016/j.prp.2026.156543},
pmid = {42166940},
issn = {1618-0631},
mesh = {Humans ; *Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; *Tumor Microenvironment/genetics ; Multiomics ; Animals ; },
abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.},
}

Humans
*Neoplasms/microbiology/genetics
*Microbiota/genetics
*Metagenomics/methods
*Tumor Microenvironment/genetics
Multiomics
Animals

@article {pmid42235263,
year = {2026},
author = {Kim, J and Müller, F and Ribeiro, CC and Dietz, C and Hero, D and Witayakran, S and Gallei, M},
title = {Cyclodextrin-modified core-shell particle synthesis and photonic crystal film formation for redox-mediated surface interaction.},
journal = {Journal of colloid and interface science},
volume = {722},
number = {},
pages = {140824},
doi = {10.1016/j.jcis.2026.140824},
pmid = {42235263},
issn = {1095-7103},
abstract = {In recent years, extensive efforts have been made to develop and utilize smart optical materials. Carbohydrate-based materials are abundant, readily accessible, and essential for advancing sustainable science and ecological cycles. Carbohydrates containing α-glycosidic linkages are naturally generated, and cyclodextrin represents a typical oligosaccharide with such a structure. The ring-shaped architecture of cyclodextrin has been widely studied because, unlike conventional chemical bonds, it enables host-guest interactions based on noncovalent binding. Incorporating cyclodextrin into nanosized, highly uniform core-shell particles could enable the production of photonic crystal films. A synthesis route for the preparation of β-cyclodextrin-modified core-shell particles with host functionality has been reported and characterized at the molecular and material levels. The molecular structures and particle-based optical film formation were validated by spectroscopic and microscopic analysis. The resulting photonic crystal films displayed vivid structural colors. Their capture property was demonstrated by a decrease in the electrochemical redox signal arising from host-guest interactions with ferrocene, while maintaining structural coloration after capture. These findings highlight the potential of the developed system for applications involving selective particle-surface interactions that can be triggered by an electrochemical response. This method will pave the way to new capturing and separation strategies and optical anti-counterfeiting technologies.},
}

@article {pmid40764303,
year = {2025},
author = {Xu, Y and Gkoutos, GV},
title = {A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {87},
pmid = {40764303},
issn = {2056-7189},
support = {101095480//HYPERMARKER/ ; 101095480//HYPERMARKER/ ; 731032//Nanocommons H2020-EU/ ; 965286//MAESTRIA/ ; 101057014//PARC/ ; HDRUK/CFC/01//MRC Heath Data Research UK/ ; },
mesh = {Animals ; *Computational Biology/methods ; Mice ; Humans ; *Microbiota ; Computer Simulation ; Machine Learning ; Gastrointestinal Microbiome ; *Ecology/methods ; Ecosystem ; Clostridioides difficile ; Clostridium Infections/microbiology ; Models, Biological ; Microbial Interactions ; },
abstract = {We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem modeling by coupling a modified generalized Lotka-Volterra formulation with machine learning optimization. Unlike traditional methods that rely on gradient matching, MBPert leverages numerical solutions of differential equations and iterative parameter estimation to robustly capture microbial dynamics. The framework is assessed within the context of two experimental scenarios: (i) paired before-and-after measurements under targeted perturbations, and (ii) longitudinal time-series data with time-dependent perturbations. Extensive simulation studies, benchmarking on standardized MTIST datasets, and application to Clostridium difficile infection in mice and repeated antibiotic perturbations of human gut micribiota, demonstrate that MBPert accurately recapitulates species interactions and predicts system dynamics. Our results highlight MBPert as a powerful and flexible tool for mechanistic insight into microbiota ecology, with broad potential applicability to other complex dynamical systems.},
}

Animals
*Computational Biology/methods
Mice
Humans
*Microbiota
Computer Simulation
Machine Learning
Gastrointestinal Microbiome
*Ecology/methods
Ecosystem
Clostridioides difficile
Clostridium Infections/microbiology
Models, Biological
Microbial Interactions

@article {pmid40770074,
year = {2025},
author = {Myers, T and Song, SJ and Chen, Y and De Pessemier, B and Khatib, L and McDonald, D and Huang, S and Gallo, R and Callewaert, C and Havulinna, AS and Lahti, L and Roeselers, G and Laiola, M and Shetty, SA and Kelley, ST and Knight, R and Bartko, A},
title = {Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1159},
pmid = {40770074},
issn = {2399-3642},
mesh = {Humans ; *Aging ; *Biometry/methods ; *Deep Learning ; *Gastrointestinal Microbiome ; *Principal Component Analysis/methods ; *Skin Microbiome ; Software Validation ; },
abstract = {Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.},
}

Humans
*Aging
*Biometry/methods
*Deep Learning
*Gastrointestinal Microbiome
*Principal Component Analysis/methods
*Skin Microbiome
Software Validation

@article {pmid40770961,
year = {2026},
author = {Lopes-Araujo, HF and Guimarães, RL and Carvalho-Silva, WHV},
title = {Correlations between new HIV infections and hospital admissions for non-Hodgkin lymphoma in Brazil.},
journal = {International journal of cancer},
volume = {158},
number = {1},
pages = {84-93},
doi = {10.1002/ijc.70076},
pmid = {40770961},
issn = {1097-0215},
mesh = {Humans ; Brazil/epidemiology ; Male ; *HIV Infections/epidemiology/complications ; Female ; *Lymphoma, Non-Hodgkin/epidemiology/virology ; Adult ; Middle Aged ; *Hospitalization/statistics & numerical data ; Adolescent ; Incidence ; Young Adult ; Aged ; Child ; },
abstract = {Despite advancements in antiretroviral therapy, human immunodeficiency virus (HIV) infections remain a significant global health challenge. With increasing life expectancy among people living with HIV, the emergence of HIV-related malignancies, notably non-Hodgkin lymphoma (NHL), has become a prominent concern. This study aims to investigate the correlation between new HIV infections and NHL hospitalizations in Brazil from 2010 to 2022. Using an ecological time series design, data from authoritative sources, including the Notifiable Diseases Information System and the Department of Unified Health System Informatics, were analyzed. The study cohort comprised individuals admitted to the Brazilian Unified Health System, categorized by geographical region, sex, and age cohorts. Pearson's and Spearman's correlation coefficients were utilized to examine the correlation between new HIV infections and NHL hospitalizations. Our analysis revealed a strong positive and statistically significant correlation between the incidence of new HIV cases and NHL hospitalizations in Brazil (r = 0.8901; p = .0001) and in most regions (r > 0.80; p < .001). Moreover, our findings indicate that this correlation becomes evident from the age of 15 onward, with a discernible tendency to escalate with advancing age from moderate to very strong (r > 0.62; p < .02). Regarding sex, the observed correlations were strong positive for male (r = 0.8681; p = .0003) and female (r = 0.7912; p = .0020). These results underscore the importance of vigilant monitoring for individuals living with HIV. Furthermore, we emphasize the importance of rigorous screening practices and adherence to antiretroviral therapy, which may hold promising implications for managing neoplastic conditions.},
}

Humans
Brazil/epidemiology
Male
*HIV Infections/epidemiology/complications
Female
*Lymphoma, Non-Hodgkin/epidemiology/virology
Adult
Middle Aged
*Hospitalization/statistics & numerical data
Adolescent
Incidence
Young Adult
Aged
Child

@article {pmid40772542,
year = {2025},
author = {Reddy, S and Wacker, K and Fahmy, M and Hekkala, E and Bates, JM and Goodman, SM and Hackett, SJ and Raherilalao, MJ and Maddox, JD},
title = {VoronaGasyCodes: A Public Database of Mitochondrial Barcodes for Malagasy Birds.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70027},
pmid = {40772542},
issn = {1755-0998},
mesh = {Animals ; Madagascar ; *Birds/genetics/classification ; *DNA Barcoding, Taxonomic/methods ; *DNA, Mitochondrial/genetics/chemistry ; Biodiversity ; *Databases, Genetic ; },
abstract = {Molecular tools are increasingly being used to survey the presence of biodiversity and their interactions within ecosystems. Indirect methods, like environmental DNA (eDNA) and invertebrate-derived DNA (iDNA), are dependent on sequence databases with accurate and sufficient taxonomic representation. These methods are increasingly being used in regions and habitats where direct detection or observations can be difficult for a variety of reasons. Madagascar is a biodiversity hotspot with a high proportion of endemic species, many of which are threatened or endangered. Here we describe a new resource, VoronaGasyCodes, a curated database of newly published genetic sequences from Malagasy birds. Our database is currently populated with six mitochondrial genes or DNA barcodes for 142 species including 70% of the birds endemic to the island and will be periodically updated as new data become available. We demonstrate the utility of our database with an iDNA study of leech blood meals where we successfully identified 77% of the hosts to species. These types of resources for characterising biodiversity are critical for insights into species distribution, discovery of new taxa, novel ecological connections and advancing conservation and restoration measures.},
}

Animals
Madagascar
*Birds/genetics/classification
*DNA Barcoding, Taxonomic/methods
*DNA, Mitochondrial/genetics/chemistry
Biodiversity
*Databases, Genetic

@article {pmid40772610,
year = {2025},
author = {Tsuji, S and Kunimatsu, S and Watanabe, K},
title = {Environmental DNA Comparative Phylogeography: Simultaneous Estimation of Population Structures Within a Species-Rich Group of Freshwater Gobies.},
journal = {Molecular ecology},
volume = {34},
number = {18},
pages = {e70059},
doi = {10.1111/mec.70059},
pmid = {40772610},
issn = {1365-294X},
support = {23K13967//Japan Society for the Promotion of Science/ ; //ESPEC Foundation for Global Environment Research and Technology/ ; },
mesh = {Phylogeography ; Animals ; *DNA, Environmental/genetics ; Fresh Water ; Japan ; *Genetics, Population ; Haplotypes ; *Perciformes/genetics/classification ; Cytochromes b/genetics ; Phylogeny ; Biodiversity ; DNA, Mitochondrial/genetics ; Genetic Variation ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Comparative phylogeography provides crucial insights into evolutionary processes shaping biodiversity patterns by analysing spatial genetic variations across multiple species. However, conventional capture-based methods are often labour-intensive, particularly for multi-species analyses. Environmental DNA (eDNA) analysis has significant advantages in comparative phylogeography, including simplified field surveys requiring only water collection and the potential to simultaneously analyse multiple species from a single sample. To further expand the eDNA application and demonstrate its utility in comparative phylogeographic studies, this study employed eDNA analysis to simultaneously analyse the phylogeographic patterns in a species-rich freshwater goby group (Rhinogobius) in the Japanese Archipelago. DNA amplification was performed on eDNA samples collected from 573 sites across the archipelago using newly designed group-specific primers targeting the mitochondrial cytochrome b region of Rhinogobius. High-throughput sequencing detected haplotypes of all nine known species (or species groups) occurring in this region, followed by phylogenetic and network analyses. The eDNA analysis successfully revealed the genetic population structures across multiple species. A landlocked species, R. flumineus, exhibited fine-scale population differentiation shaped by geomorphological barriers, while amphidromous species showed broader genetic patterns likely influenced by ocean currents and their ecological traits. The phylogenetic and phylogeographic patterns reconstructed by the eDNA analysis were almost completely concordant with previously identified patterns of limited groups based on conventional methods, demonstrating the reliability of eDNA-based comparative phylogeography. This study highlights the potential of eDNA to complement and partially replace conventional methods, facilitating large-scale comparative phylogeographic research to gain new insights into spatial patterns and evolutionary processes of biodiversity.},
}

Phylogeography
Animals
*DNA, Environmental/genetics
Fresh Water
Japan
*Genetics, Population
Haplotypes
*Perciformes/genetics/classification
Cytochromes b/genetics
Phylogeny
Biodiversity
DNA, Mitochondrial/genetics
Genetic Variation
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing

@article {pmid40774342,
year = {2025},
author = {Cao, W and Cao, X and Sutherland, AD},
title = {Planning for the Unexpected and Unintended Effects of mHealth Interventions: Systematic Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e68909},
pmid = {40774342},
issn = {1438-8871},
mesh = {*Telemedicine ; Humans ; },
abstract = {BACKGROUND: Mobile health (mHealth) interventions can produce both intended and unintended effects. Examining these unintended effects helps create a more complete and objective understanding of mHealth interventions and can reduce potential harm to participants. Existing studies on the unintended effects, which were published several years ago, tend to have either a general focus on health IT or a specific focus on health care providers, thereby excluding other key stakeholders (eg, patients and community health workers). Additionally, these studies did not systematically outline the causes of the unintended effects or strategies for their prevention.

OBJECTIVE: To address this gap, this systematic review, guided by the ecological framework, aims to systematically identify the unintended effects of mHealth interventions, create a typology for them, investigate the reasons for their occurrence, describe how they were detected, and propose ways to prevent or lessen them.

METHODS: Following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to examine the unintended effects of health interventions that use mobile technology.

RESULTS: A total of 15 papers were included in the review. An ecological typology of mHealth intervention unintended effects (mHUE) was developed, which includes 26 distinct effects (eg, silencing and boomerang). The majority of these unintended effects (n=20) occur at the individual level and span physical or behavioral (n=7), psychological (n=8), cognitive (n=4), and financial (n=1) domains. Three effects occur at the interpersonal level and another 3 at the community or institutional level. Most of the identified effects (n=22) were negative. Potential causes for these effects include the improper use of mHealth technology, poorly designed interventions, the application of unsuitable intervention mechanisms, or a misalignment between the intended outcomes and the sociocultural context. Strategies and recommendations (eg, considering the context such as cultural norms) were suggested to help prevent or reduce the unintended effects.

CONCLUSIONS: The unintended effects detailed in the mHUE typology were heterogenous and context-dependent. These effects can influence individuals across different domains and also affect unintended people within the ecological system. As most of the unintended effects are negative, if they are not monitored, mHealth interventions designed to empower participants could paradoxically disempower them (eg, decreasing self-efficacy for disease management, undermining patient control, and engagement). The mHUE typology, together with the proposed recommendations and strategies, can be used as a guide to enhance the planning, design, implementation, and postimplementation evaluation on mHealth interventions. Future research should concentrate on understanding the specific mechanisms behind these unintended effects.},
}

*Telemedicine
Humans

@article {pmid40774411,
year = {2025},
author = {Zhang, L and Liu, Y and Chen, K and Yue, Q and Wang, C and Xie, L and Molnár, I and Xu, Y},
title = {Genome mining of tailoring enzymes from biosynthetic gene clusters for synthetic biology: A case study with fungal methyltransferases.},
journal = {Metabolic engineering},
volume = {92},
number = {},
pages = {125-135},
doi = {10.1016/j.ymben.2025.08.001},
pmid = {40774411},
issn = {1096-7184},
mesh = {*Methyltransferases/genetics/metabolism ; *Multigene Family ; *Genome, Fungal ; *Fungal Proteins/genetics/metabolism ; *Synthetic Biology/methods ; *Fungi/genetics/enzymology ; *Data Mining/methods ; Biosynthetic Pathways/genetics ; Biological Products/metabolism ; },
abstract = {Harnessing the potential of tailoring enzymes within fungal natural product (NP) biosynthetic gene clusters (BGCs) can significantly enhance NP diversity and production efficiency via artificially constructed microbial cell factories. To achieve this, an efficient genome mining method is crucial, especially since the functions of many putative enzymes in databases are unknown. As a test case, we aimed to identify methyltransferases (MTs) that modify a polyketide substrate without a known cognate MT. 16,748 putative MTs were annotated in 101,321 fungal BGCs and grouped into orthologous families. Three methods were explored to prioritize suitable enzymes. Among these, the machine learning method proved superior, with 11 out of 15 tested MTs successfully methylating the test substrate. This demonstrates the effectiveness of machine learning to mine tailoring enzymes that modify selected compounds, aiding synthetic biology in optimizing NP biosynthesis and facilitating the production of "unnatural products" for pharmaceutical or other bioindustrial applications.},
}

*Methyltransferases/genetics/metabolism
*Multigene Family
*Genome, Fungal
*Fungal Proteins/genetics/metabolism
*Synthetic Biology/methods
*Fungi/genetics/enzymology
*Data Mining/methods
Biosynthetic Pathways/genetics
Biological Products/metabolism

@article {pmid40774560,
year = {2025},
author = {Guo, J and Lei, W and Liang, X and Wang, H and Qi, W and Huang, S and Chen, X and He, S},
title = {Three-dimensional distribution and key drivers of neonicotinoid residues in hilly agricultural areas.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122524},
doi = {10.1016/j.envres.2025.122524},
pmid = {40774560},
issn = {1096-0953},
mesh = {*Neonicotinoids/analysis ; *Soil Pollutants/analysis ; *Insecticides/analysis ; *Environmental Monitoring ; Agriculture ; *Pesticide Residues/analysis ; Soil/chemistry ; China ; Nitro Compounds/analysis ; Guanidines/analysis ; Thiazoles ; },
abstract = {Neonicotinoids (NNIs) raise global concern due to their substantial soil residues and potential health risks to animal and human health. High water solubility and low soil adsorption enhanced vertical and horizontal migration of NNIs. However, understanding of NNIs' three-dimensional distribution in soils and influencing factors remains limited, limiting accurate risk assessment and remediation strategies for agriculture ecosystems. This study selected typical mountainous farmland soil to investigate the three-dimensional distribution of NNIs contents and composition. The findings indicated that the average detection rate of imidacloprid (IMI) in the 0-20 cm layer was 33 % higher than that in the 30-40 cm layer, whereas clothianidin (CLO) detection rates remained consistent across 0-40 cm layer. The contents of eight NNIs (∑8NNIs) in the study area ranged from 0.09 to 37.08 ng/g, with the 6.58 ± 8.65 ng/g in the 0-10 cm and 2.60 ± 7.78 ng/g in the 30-40 cm layer. The contents of ∑8NNIs, IMI, and CLO decreased by 60 %, 62 %, and 75 %, respectively, with increasing depth. The proportion of IMI and CLO to ∑8NNIs decreased and increased by 35 % and 12 %, respectively, in the 0-40 cm soil, leading to IMI predominance in the topsoil (60 %) and CLO in the deeper soil (29 %). Correlation analysis revealed that soil particle size, slope, and elevation were significantly associated with both the ∑8NNIs and the proportions of IMI and CLO. These results highlighted the substantial influence of topography and soil structure on the vertical distribution of NNIs. Additionally, the ∑8NNIs content in stem mustard soil was higher than in sweet potato, rice, corn, and forest. Overall, the study found very low health risks to humans (hazard index, HI < 1) and no overall potential ecological risk in the study area, though localized sublethal risks to non-target organisms were identified. Furthermore, the spatial correlation between IMI and CLO health risk regions identified overlapping high-risk areas.},
}

*Neonicotinoids/analysis
*Soil Pollutants/analysis
*Insecticides/analysis
*Environmental Monitoring
Agriculture
*Pesticide Residues/analysis
Soil/chemistry
China
Nitro Compounds/analysis
Guanidines/analysis
Thiazoles

@article {pmid40774918,
year = {2025},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santsch, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Corrigendum to "Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050" [Mar. Pollut. Bull. 206 (2024) 116664].},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118543},
doi = {10.1016/j.marpolbul.2025.118543},
pmid = {40774918},
issn = {1879-3363},
}

@article {pmid40776104,
year = {2025},
author = {Bauberg, H and Tachnai, N and Hanan, G and Nehama, D and Tamburis, O and Darmoni, S and Grosjean, J and Benis, A},
title = {Automated Elicitation of Human and Ecological Health Indicators: An LLM-Based Practical Implementation for One Digital Health.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1488-1492},
doi = {10.3233/SHTI251086},
pmid = {40776104},
issn = {1879-8365},
mesh = {Humans ; *One Health ; *Health Status Indicators ; *Environmental Health/methods ; Digital Health ; },
abstract = {This paper presents a new method for automating the identification of human and ecological health indicators using the One Digital Health framework, which combines One Health and Digital Health principles. By applying mainly Large Language Models, we conduct a systematic literature review on urban freshwater environments. This automation streamlines the process of finding and analyzing relevant research, allowing us to extract vital health indicators related to urban aquatic ecosystems and human wellness. The findings support the OneAquaHealth project's goals, enhancing environmental monitoring and linking human, animal, and environmental health in a digital context.},
}

Humans
*One Health
*Health Status Indicators
*Environmental Health/methods
Digital Health

@article {pmid40777262,
year = {2025},
author = {Weiss, AS and Santos-Santiago, JA and Keenan, O and Smith, AB and Knight, M and Zackular, JP and Tamayo, R},
title = {Enterococcus faecalis modulates phase variation in Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40777262},
issn = {2692-8205},
support = {R01 AI143638/AI/NIAID NIH HHS/United States ; R01 AI188648/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; },
abstract = {To adapt and persist in the gastrointestinal tract, many enteric pathogens, including Clostridioides difficile, employ strategies such as phase variation to generate phenotypically heterogeneous populations. Notably, the role of the gut microbiota and polymicrobial interactions in shaping population heterogeneity of invading pathogens has not been explored. Here, we show that Enterococcus faecalis, an opportunistic pathogen that thrives in the inflamed gut during C. difficile infection, can impact the phase variable CmrRST signal transduction system in C. difficile. The CmrRST system controls multiple phenotypes including colony morphology, cell elongation, and cell chaining in C. difficile. Here we describe how interactions between E. faecalis and C. difficile on solid media lead to a marked shift in C. difficile phenotypes associated with phase variation of CmrRST. Specifically, E. faecalis drives a switch of the C. difficile population to the cmr-ON state leading to chaining and a rough colony morphology. This phenomenon preferentially occurs with E. faecalis among the enterococci, as other enterococcal species do not show a similar effect, suggesting that the composition of the polymicrobial environment in the gut is likely critical to shaping C. difficile population heterogeneity. Our findings shed light on the complex role that microbial ecology and polymicrobial interactions can have in the phenotypic heterogeneity of invading pathogens.},
}

@article {pmid40778113,
year = {2025},
author = {Sprint, G and Schmitter-Edgecombe, M and Weaver, R and Wiese, L and Cook, DJ},
title = {CogProg: Utilizing Large Language Models to Forecast In-the-moment Health Assessment.},
journal = {ACM transactions on computing for healthcare},
volume = {6},
number = {2},
pages = {},
pmid = {40778113},
issn = {2637-8051},
support = {R01 AG066748/AG/NIA NIH HHS/United States ; R01 AG083925/AG/NIA NIH HHS/United States ; R25 AG046114/AG/NIA NIH HHS/United States ; R01 AG065218/AG/NIA NIH HHS/United States ; R35 AG071451/AG/NIA NIH HHS/United States ; R01 EB009675/EB/NIBIB NIH HHS/United States ; },
abstract = {Forecasting future health status is beneficial for understanding health patterns and providing anticipatory support for cognitive and physical health difficulties. In recent years, generative large language models (LLMs) have shown promise as forecasters. Though not traditionally considered strong candidates for numeric tasks, LLMs demonstrate emerging abilities to address various forecasting problems. They also provide the ability to incorporate unstructured information and explain their reasoning process. In this paper, we explore whether LLMs can effectively forecast future self-reported health state. To do this, we utilized in-the-moment assessments of mental sharpness, fatigue, and stress from multiple studies, utilizing daily responses (N=106 participants) and responses that are accompanied by text descriptions of activities (N=32 participants). With these data, we constructed prompt/response pairs to predict a participant's next answer. We fine-tuned several LLMs and applied chain-of-thought prompting evaluating forecasting accuracy and prediction explainability. Notably, we found that LLMs achieved the lowest mean absolute error (MAE) overall (0.851), while gradient boosting achieved the lowest overall root mean squared error (RMSE) (1.356). When additional text context was provided, LLM forecasts achieved the lowest MAE for predicting mental sharpness (0.862), fatigue (1.000), and stress (0.414). These multimodal LLMs further outperformed the numeric baselines in terms of RMSE when predicting stress (0.947), although numeric algorithms achieved the best RMSE results for mental sharpness (1.246) and fatigue (1.587). This study offers valuable insights for future applications of LLMs in health-based forecasting. The findings suggest that LLMs, when supplemented with additional text information, can be effective tools for improving health forecasting accuracy.},
}

@article {pmid40779849,
year = {2025},
author = {Zhu, J and Ding, X and Xu, Q and Fan, Y and Zhu, P and Li, X and Zhang, X and Zhang, Q and Du, X and Zhou, W and Jiao, J and Lu, B and Lu, C},
title = {Insights into the disinfection byproduct bromochloroacetamide-induced cardiotoxicity of zebrafish embryo-larvae: A multiomics approach and comparison of biomarker responsiveness.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118805},
doi = {10.1016/j.ecoenv.2025.118805},
pmid = {40779849},
issn = {1090-2414},
mesh = {Animals ; *Zebrafish/embryology ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Cardiotoxicity/etiology ; *Acetamides/toxicity ; Embryo, Nonmammalian/drug effects ; Larva/drug effects ; *Disinfectants/toxicity ; Heart/drug effects ; Metabolomics ; Disinfection ; Multiomics ; },
abstract = {Bromochloroacetamide (BCAcAm), an inevitable byproduct of the water treatment disinfection process, is widely detected in drinking water. Previous toxicological and in silico results suggested that developmental effects are associated with analogous chemical exposure; however, the key molecular events and underlying mechanisms remain unclear, especially in the early stages of aquatic organisms. In the present study, a zebrafish larval model was used to comprehensively assess the developmental toxicity of BCAcAm via transcriptional, metabolic, biochemical and morphological tests. Integration analyses of RNA sequencing and untargeted metabolomic data revealed crucial biological processes related to drug metabolism, cardiac muscle contraction and oxidative phosphorylation, which started from the initial stage, and ferroptosis progressed to the advanced stage in validated cardiac defects. Biochemical assays further verified ATP depletion, ROS and MDA accumulation, and hyperactivation of detoxification (increased GST activity) and the antioxidative system (increased GSH and GSSG levels). Transcriptionally, BCAcAm led to gpx4 downregulation, iron homeostasis perturbation (upregulated tfr and tf and downregulated fth) and lipid peroxidation (elevated alox12 and lpcat3), suggesting the involvement of ferroptosis. Moreover, the application of Fer-1 (a ferroptosis inhibitor) reversed BCAcAm-induced mitochondrial dysfunction and subsequent cardiotoxicity. In addition, the BMD and IBRv2 indices were derived from molecules across various biological levels. The general ranking of the different biomarkers in terms of better responsiveness and sensitivity performance is as follows: transcriptomics > metabolomics > biochemical assays. In the present study, an approach to detecting chemical-induced adverse outcomes and deciphering the underlying mechanisms through high-throughput data analysis is applied. This study provides valuable insights into the responsiveness and sensitivity of biomarkers, which may be instrumental for evaluating the ecological and health risks associated with newly emerged contaminants.},
}

Animals
*Zebrafish/embryology
Biomarkers/metabolism
*Water Pollutants, Chemical/toxicity
*Cardiotoxicity/etiology
*Acetamides/toxicity
Embryo, Nonmammalian/drug effects
Larva/drug effects
*Disinfectants/toxicity
Heart/drug effects
Metabolomics
Disinfection
Multiomics

@article {pmid40781089,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1385},
doi = {10.1038/s41597-025-05752-9},
pmid = {40781089},
issn = {2052-4463},
support = {R44 CA278140/CA/NCI NIH HHS/United States ; R44 HD104323/HD/NICHD NIH HHS/United States ; },
}

@article {pmid40781446,
year = {2025},
author = {Rauniyar, S and Samanta, D and Thakur, P and Saxena, P and Singh, RN and Bazin, A and Bomgni, A and Fotseu, E and Etienne, GZ and Gadhamshetty, V and Peyton, BM and Fields, M and Subramaniam, M and Sani, RK},
title = {Mapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {305},
pmid = {40781446},
issn = {1573-0972},
support = {5P20GM103443-20/NH/NIH HHS/United States ; 1736255//National Science Foundation/ ; },
mesh = {*Desulfovibrio/genetics/metabolism/classification ; *Genome, Bacterial ; *Sulfates/metabolism ; Phylogeny ; Multigene Family ; Gene Regulatory Networks ; Genes, Bacterial ; Gene Ontology ; },
abstract = {The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.},
}

*Desulfovibrio/genetics/metabolism/classification
*Genome, Bacterial
*Sulfates/metabolism
Phylogeny
Multigene Family
Gene Regulatory Networks
Genes, Bacterial
Gene Ontology

@article {pmid40782603,
year = {2025},
author = {Benvenuti, MC and Merkle, EC and McCarthy, DM},
title = {Physical context of alcohol use and craving: An EMA exploratory study.},
journal = {Addictive behaviors},
volume = {170},
number = {},
pages = {108450},
pmid = {40782603},
issn = {1873-6327},
support = {R01 AA019546/AA/NIAAA NIH HHS/United States ; T32 AA013526/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Craving ; Male ; Female ; *Ecological Momentary Assessment ; *Alcohol Drinking/psychology/epidemiology ; Adult ; Young Adult ; Adolescent ; Geographic Information Systems ; Self Report ; },
abstract = {While environmental and physical contextual factors play an important role in alcohol use and motivation for use, assessment of the physical context of use, even when using ecological momentary assessments (EMA), has been limited. While EMA research has examined drinking locations at the event level using categories of drinking locations, there is considerable within-category variability in the attributes of drinking locations. Using data from a 6-week EMA study (N = 207), this exploratory study sought to determine drinking locations through the combination of EMA self-report and GPS coordinates. Through multilevel modeling, we also tested whether specific locations were associated with variability in drinking (self-reported drinking and breathalyzer readings) and craving for alcohol. Results indicated significant differences in both alcohol consumption and craving between home, friend's houses, and on-premises drinking locations. Our results offer proof of concept for using mobile and geospatial data to passively identify on-premise drinking locations. This approach has the potential to aid in the development of targeted intervention strategies that identify and mitigate risks associated with specific drinking environments.},
}

Humans
*Craving
Male
Female
*Ecological Momentary Assessment
*Alcohol Drinking/psychology/epidemiology
Adult
Young Adult
Adolescent
Geographic Information Systems
Self Report

@article {pmid40786600,
year = {2025},
author = {Boyes, D and Gardiner, A and , and , and , and , and , and , and , and , },
title = {The genome sequence of the V-Pug moth, Chloroclystis v-ata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {197},
pmid = {40786600},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Chloroclystis v-ata (V-Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 275.35 megabases. Most of the assembly (99.95%) is scaffolded into 17 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.49 kilobases.},
}

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {967},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

*Metagenomics/methods
*Ecosystem
Microbiota/genetics
*Water Microbiology
Environmental Monitoring/methods
Computational Biology/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Metagenome

@article {pmid40794746,
year = {2025},
author = {Alkhatib, SA and Arya, S and Islayem, D and Nyadzayo, RM and Mohamed, S and Yousef, AF and Hernandez, HH and Pappa, AM},
title = {Revealing bioremediation potential of novel indigenous bacteria from oil-contaminated sites in the UAE: A combined bioinformatics and experimental validation.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329515},
pmid = {40794746},
issn = {1932-6203},
mesh = {*Biodegradation, Environmental ; *Computational Biology/methods ; United Arab Emirates ; Polycyclic Aromatic Hydrocarbons/metabolism ; *Bacteria/metabolism/genetics/isolation & purification ; Phenols/metabolism ; *Soil Pollutants/metabolism ; },
abstract = {Microbial biodegradation of recalcitrant aromatic hydrocarbon pollutants represents an environmentally sustainable strategy for remediating contaminated sites. However, elucidating the metabolic capabilities and genetic determinants of biodegrading strains is crucial for optimizing bioremediation strategies. In this study, we comprehensively characterize the aromatic catabolic potential of two indigenous bacterial isolates, A. xylosoxidans C2 (A. x. C2) and A. xylosoxidans KW38 (A. x. KW38), obtained from hydrocarbon-impacted environments in the United Arab Emirates (UAE). Experimental validation through aromatic hydrocarbons supplemented growth studies confirmed the capability of the isolated bacteria to mineralize bisphenol A, 4-hydroxybenzoic acid, 1-naphthalenemethanol, and the high molecular weight polycyclic aromatic hydrocarbon (PAH), pyrene, in the presence of glucose. Their degradation efficiencies were comparable to or greater than those of Pseudomonas paraeruginosa, a well-characterized model organism for aromatic compound degradation. Integrated bioinformatic analyses uncovered fundamental aromatic catabolic pathways conserved across Achromobacter species, along with strain-specific genes that potentially confer specialized degradative capacities, highlighting the genomic basis of the observed metabolic versatility. Further, protein modeling based on the curated sequences revealed unique features of individual catabolic enzymes and their interaction networks. Notably, a dehydrogenase enzyme involved in aromatic ring cleavage was identified exclusively in these UAE isolates. These findings establish A. x. C2 and A. x. KW38 as promising bioremediators of diverse aromatic pollutants. Overall, the study exemplifies a powerful and comprehensive methodological framework that bridges bioinformatic analysis and experimental research to further optimize the effectiveness of experimental design. We achieved a substantial reduction in the number of unknown genetic and metabolic determinants of aromatic hydrocarbon degradation in the strains, reducing uncertainty by 99.3%, thereby enhancing the overall process and outcomes for systematic biodiscovery of pollutant-degrading environmental microbes to address ecological challenges.},
}

*Biodegradation, Environmental
*Computational Biology/methods
United Arab Emirates
Polycyclic Aromatic Hydrocarbons/metabolism
*Bacteria/metabolism/genetics/isolation & purification
Phenols/metabolism
*Soil Pollutants/metabolism

@article {pmid40796553,
year = {2025},
author = {Arehart, CH and Lin, M and Gibson, RA and , and Raghavan, S and Gignoux, CR and Stanislawski, MA and Grotzinger, AD and Evans, LM},
title = {Modeling the genomic architecture of adiposity and anthropometrics across the lifespan.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7494},
pmid = {40796553},
issn = {2041-1723},
support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 AG046938/AG/NIA NIH HHS/United States ; T32 MH016880/MH/NIMH NIH HHS/United States ; RF1 AG073593/AG/NIA NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 MH120219/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Adiposity/genetics ; Male ; Female ; Genome-Wide Association Study ; *Obesity/genetics ; Multifactorial Inheritance ; Adult ; Middle Aged ; Anthropometry ; *Longevity/genetics ; Genomics ; Polymorphism, Single Nucleotide ; Aged ; Body Size/genetics ; },
abstract = {Obesity-related conditions are among the leading causes of preventable death and are increasing in prevalence worldwide. Body size and composition are complex traits that are challenging to characterize due to environmental and genetic influences, longitudinal variation, heterogeneity between sexes, and differing health risks based on adipose distribution. Here, we construct a 4-factor genomic structural equation model using 18 measures, unveiling shared and distinct genetic architectures underlying birth size, abdominal size, adipose distribution, and adiposity. Multivariate genome-wide associations reveal the adiposity factor is enriched specifically in neural tissues and pathways, while adipose distribution is enriched more broadly across physiological systems. In addition, polygenic scores for the adiposity factor predict many adverse health outcomes, while those for body size and composition predict a more limited subset. Finally, we characterize the factors' genetic correlations with obesity-related traits and examine the druggable genome by constructing a bipartite drug-gene network to identify potential therapeutic targets.},
}

Humans
*Adiposity/genetics
Male
Female
Genome-Wide Association Study
*Obesity/genetics
Multifactorial Inheritance
Adult
Middle Aged
Anthropometry
*Longevity/genetics
Genomics
Polymorphism, Single Nucleotide
Aged
Body Size/genetics

@article {pmid40796641,
year = {2025},
author = {Sanad, H and Moussadek, R and Mouhir, L and Lhaj, MO and Dakak, H and Manhou, K and Zouahri, A},
title = {Monte carlo simulation for evaluating spatial dynamics of toxic metals and potential health hazards in sebou basin surface water.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29471},
pmid = {40796641},
issn = {2045-2322},
mesh = {Monte Carlo Method ; Humans ; *Metals, Heavy/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; Risk Assessment ; *Environmental Monitoring/methods ; Morocco ; Geographic Information Systems ; Principal Component Analysis ; },
abstract = {Surface water is vital for environmental sustainability and agricultural productivity but is highly vulnerable to heavy metals (HMs) pollution from human activities. The focus of this research is to provide an analysis of ecological and human exposure to HMs in the Sebou Basin, an agriculturally significant region within Morocco's Gharb Plain. Using a multi-index integration approach, encompassing HM pollution indices, Human Health Risk Assessment (HHRA), Monte Carlo Simulation (MCS), multivariate statistical analysis (MSA), and Geographic Information Systems (GIS), twenty samples of surface water were taken and subjected to analysis. The results demonstrated notable spatial variability, with the northwestern, southwestern, and western parts of the Sebou Basin showing higher contamination levels. Cu exhibited the highest hazard quotient for ingestion, while Cr exceeded the hazard index (HI) threshold in both age categories. Statistical analysis uncovered strong associations, particularly between As and Cr, while principal component analysis (PCA) detected two key factors explaining 74.44% of the overall variability. Pollution indices classified all samples as highly contaminated (HPI > 30), with 65% categorized as "seriously affected" (MI > 6). The HHRA results indicated a heightened non-carcinogenic risk for children and carcinogenic risks exceeding acceptable thresholds (TCR > 10[-4]), with Ni presenting the highest risk (TCR = 2.32 × 10[-3] for children). MCS results revealed that Cu and Cr pose potential risks, with Cu exceeding the safety threshold for ingestion in both adults and children. These results emphasize the urgent necessity for tailored strategies to reduce contamination and foster sustainable agricultural and environmental management practices.},
}

Monte Carlo Method
Humans
*Metals, Heavy/analysis/toxicity
*Water Pollutants, Chemical/analysis/toxicity
Risk Assessment
*Environmental Monitoring/methods
Morocco
Geographic Information Systems
Principal Component Analysis

@article {pmid40797121,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {9},
pages = {257},
pmid = {40797121},
issn = {1554-3528},
support = {UL1 TR002378/TR/NCATS NIH HHS/United States ; UL1TR002378/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Adult ; *Voice ; Young Adult ; *Mobile Applications ; *Speech ; Middle Aged ; Adolescent ; },
abstract = {This article reports on the validation of Fabla, a researcher-developed and university-hosted smartphone app that facilitates naturalistic and secure collection of participants' spoken responses to researcher questions. Fabla was developed to meet the need for tools that (a) collect longitudinal qualitative data and (b) capture speech biomarkers from participants' natural environments. This study put Fabla to its first empirical test using a repeated-measures experimental design in which participants (n = 87) completed a 1-week voice daily diary via the Fabla app, and an identical 1-week text-entry daily diary administered via Qualtrics, with diary method order counterbalanced and randomized. A preregistered analysis plan investigated (1) adherence, usability, and acceptability of Fabla, (2) concurrent validity of voice diaries (vs. text-entry diaries) by comparing linguistic features obtained via each diary method, and (3) differences in the strength of the association between linguistic features and their known psychological correlates when assessed by voice versus text-entry diary. Voice diaries yielded more than double the mean daily language volume (word count) compared to text-entry diaries and received high usability and acceptability ratings. Linguistic markers consistently associated with depression in prior research were significantly associated with depression symptoms when assessed via voice but not text-entry diaries, and the difference in correlation magnitude was significant. Word-count-adjusted linguistic patterns were highly correlated between diary methods, with statistically significant mean differences observed for some linguistic dimensions in the presence of these associations. Fabla is a promising tool for collecting high-quality speech data from participants' naturalistic environments, overcoming multiple limitations of text-entry responding.},
}

Humans
Female
Male
Adult
*Voice
Young Adult
*Mobile Applications
*Speech
Middle Aged
Adolescent

@article {pmid40798830,
year = {2025},
author = {Abraham, AJ and Clauss, M and Bailey, MA and Duvall, ES},
title = {Body Mass Scaling of Sodium Regulation in Mammals.},
journal = {Acta physiologica (Oxford, England)},
volume = {241},
number = {9},
pages = {e70090},
doi = {10.1111/apha.70090},
pmid = {40798830},
issn = {1748-1716},
}

@article {pmid40800427,
year = {2024},
author = {Merritt, H and Faskowitz, J and Gonzalez, MZ and Betzel, RF},
title = {Stability and variation of brain-behavior correlation patterns across measures of social support.},
journal = {Imaging neuroscience (Cambridge, Mass.)},
volume = {2},
number = {},
pages = {},
pmid = {40800427},
issn = {2837-6056},
abstract = {The social environment has a critical influence on human development, cognition, and health. Research in health psychology and social neuroscience indicate an urgent need to understand how social relationships are associated with brain function and organization. To address this, we apply multilayer modeling and modularity maximization-both established tools in network neuroscience-to jointly cluster patterns of brain-behavior associations for seven social support measures. By using network approaches to map and analyze the connectivity between all pairs of brain regions simultaneously, we can clarify how relationships between brain regions (e.g. connectivity) change as a function of social relationships. This multilayer approach enables direct comparison of brain-behavior associations across social contexts for all brain regions and builds on both ecological and developmental neuroscientific findings and network neuroscientific approaches. In particular, we find that subcortical and control systems are especially sensitive to different constructs of perceived social support. Network nodes in these systems are highly flexible; their community affiliations, which reflect groups of nodes with similar patterns of brain-behavior associations, differ across social support measures. Additionally, our application of multilayer modeling to patterns of brain-behavior correlations, as opposed to just functional connectivity, represents an innovation in how multilayer models are used in human neuroscience. More than that, it offers a generalizable technique for studying the stability and variation of brain-behavior associations.},
}

@article {pmid40801436,
year = {2025},
author = {Karaman, MZ and Yetiman, AE and Zhan, J and Fidan, O},
title = {Biochemical Characterization and Genome Analysis of Pseudomonas loganensis sp. nov., a Novel Endophytic Bacterium.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70051},
pmid = {40801436},
issn = {2045-8827},
support = {//This study was financially supported by The Scientific and Technological Research Council of Turkiye (TUBITAK) (Grant No: 221Z280)./ ; },
mesh = {*Pseudomonas/genetics/classification/isolation & purification/drug effects/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; DNA, Bacterial/genetics/chemistry ; *Endophytes/genetics/classification/isolation & purification ; Multigene Family ; Microbial Sensitivity Tests ; Carotenoids/metabolism ; Sequence Analysis, DNA ; Computational Biology ; },
abstract = {Pseudomonas species are highly adaptable, thriving in diverse environments and exhibiting remarkable genetic and metabolic diversity. While some strains are pathogenic, others have significant ecological and industrial applications. Bioinformatics and biochemical analyses, including antibiotic sensitivity testing, revealed that Pseudomonas loganensis sp. nov. can tolerate NaCl concentrations up to 5% and pH ranges between 5 and 9. Antibiogram results corroborated genome data, demonstrating resistance to vancomycin, ampicillin, methicillin, oxacillin, and penicillin G. Phylogenetic analysis based on 16S rRNA, rpoB, rpoD, and gyrB genes, combined with average nucleotide identity (ANI) comparisons, confirmed P. loganensis sp. nov. as a novel species within the Pseudomonas genus. Genome analysis further revealed the presence of turnerbactin and carotenoid gene clusters. Turnerbactin, known to contribute to nitrogen fixation in plants, highlights the strain's potential as a biofertilizer. Additionally, the carotenoid gene cluster suggests potential applications in industrial carotenoid production. The discovery of a trehalose synthase (treS) gene indicates the capability for one-step conversion of maltose into trehalose, underscoring its potential utility in trehalose production.},
}

*Pseudomonas/genetics/classification/isolation & purification/drug effects/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
*Genome, Bacterial
Anti-Bacterial Agents/pharmacology
DNA, Bacterial/genetics/chemistry
*Endophytes/genetics/classification/isolation & purification
Multigene Family
Microbial Sensitivity Tests
Carotenoids/metabolism
Sequence Analysis, DNA
Computational Biology

@article {pmid40803399,
year = {2025},
author = {Jin, L and Lu, Y and Huang, J and Liu, J and Wei, X and Ma, G and Yu, H},
title = {Metabolism exploration of disinfection byproducts halonitromethanes (HNMs) by cytochrome P450 enzymes and toxicity evaluation.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122575},
doi = {10.1016/j.envres.2025.122575},
pmid = {40803399},
issn = {1096-0953},
mesh = {*Cytochrome P-450 Enzyme System/metabolism ; *Disinfectants/toxicity/metabolism ; Animals ; Humans ; Rats ; *Nitroparaffins/toxicity/metabolism ; Disinfection ; Microsomes, Liver/metabolism ; },
abstract = {The nitrogen-contained disinfection by-products, halonitromethanes (HNMs), are known for their high cytotoxicity and genotoxicity. Although HNMs can be metabolized by cytochrome P450 enzymes (P450s), the specific mechanism has remained unclear. To shed light on this, density functional theory (DFT) calculations were performed to elucidate the potential oxidative P450-catalytic activation of the nine HNMs. Our findings reveal that active species of P450s (Cpd I) predominantly react with halogen-substituted nitromethanes via hydrogen abstraction and bromine atom abstraction, rather than chlorosylation. As a result of these reactions, oxidized HNMs are produced and can undergo further hydrolysis, leading to nitro-formaldehyde, nitro formyl halogen, halogen hydride, hypobromous acid, and nitroformic acid. To experimentally validate the computational predictions, in vitro experiments were conducted on five typical nitromethanes using human liver microsomes and the results reveal that DCNM, BCNM and DBCNM form nitroformyl chlorine (NO2CClO), while BCNM, DBNM and TBNM are transferred into nitroformyl bromide (NO2CBrO). Nitroformic acid is also identified as a metabolite in the TBNM metabolism reaction. Toxicity assessment reveals that metabolic transformation leads to an overall reduction in the ecological toxicity. However, metabolites showed similar toxicity to Fathead minnow and even higher acute toxicity to rat, as well as larger probability of hERG inhibition effects than HNMs, underscoring the need for caution in health risk assessment. By integrating in silico and in vitro approaches, this work has provided a comprehensive understanding of the metabolism of HNMs and offered potential toxicity data basis of these compounds.},
}

*Cytochrome P-450 Enzyme System/metabolism
*Disinfectants/toxicity/metabolism
Animals
Humans
Rats
*Nitroparaffins/toxicity/metabolism
Disinfection
Microsomes, Liver/metabolism

@article {pmid40805736,
year = {2025},
author = {Lu, F and Yi, B and Ma, JX and Wang, SN and Feng, YJ and Qin, K and Tu, Q and Bu, ZJ},
title = {Drought and Shrub Encroachment Accelerate Peatland Carbon Loss Under Climate Warming.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
pmid = {40805736},
issn = {2223-7747},
support = {U23A2003//The National Nature Science Foundation of China/ ; 42407354//The National Nature Science Foundation of China/ ; 42371050//The National Nature Science Foundation of China/ ; 20230203002SF and 20210402032GH//Jilin Provincial Science and Technology Development Project/ ; 2024QN1081//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Peatlands store substantial amounts of carbon (C) in the form of peat, but are increasingly threatened by drought and shrub encroachment under climate warming. However, how peat decomposition and its temperature sensitivity (Q10) vary with depth and plant litter input under these stressors remains poorly understood. We incubated peat from two depths with different degrees of decomposition, either alone or incubated with Sphagnum divinum shoots or Betula ovalifolia leaves, under five temperature levels and two moisture conditions in growth chambers. We found that drought and Betula addition increased CO2 emissions in both peat layers, while Sphagnum affected only shallow peat. Deep peat alone or with Betula exhibited higher Q10 than pure shallow peat. Drought increased the Q10 of both depths' peat, but this effect disappeared with fresh litter addition. The CO2 production rate showed a positive but marginal correlation with microbial biomass carbon, and it displayed a rather similar responsive trend to warming as the microbial metabolism quotient. These results indicate that both deep and dry peat are more sensitive to warming, highlighting the importance of keeping deep peat buried and waterlogged to conserve existing carbon storage. Additionally, they further emphasize the necessity of Sphagnum moss recovery following vascular plant encroachment in restoring carbon sink function in peatlands.},
}

@article {pmid40807726,
year = {2025},
author = {Ye, G and Yu, R},
title = {Spatiotemporal Mapping of Grazing Livestock Behaviours Using Machine Learning Algorithms.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {15},
pages = {},
pmid = {40807726},
issn = {1424-8220},
support = {Project No. 72104065//National Natural Science Foundation of China/ ; Project No. NHXXRCXM202303//Hainan New Star Projects/ ; Project No. KC20230018//Natural Resources Comprehensive Survey Command Centre Science and Technology Innovation Fund/ ; Project No. 2022KJCX04//Sanya Science and Technology Special Fund/ ; },
mesh = {Animals ; *Machine Learning ; *Livestock/physiology ; China ; Grassland ; Spatio-Temporal Analysis ; Algorithms ; Geographic Information Systems ; *Behavior, Animal/physiology ; *Herbivory/physiology ; Ecosystem ; },
abstract = {Grassland ecosystems are fundamentally shaped by the complex behaviours of livestock. While most previous studies have monitored grassland health using vegetation indices, such as NDVI and LAI, fewer have investigated livestock behaviours as direct drivers of grassland degradation. In particular, the spatial clustering and temporal concentration patterns of livestock behaviours are critical yet underexplored factors that significantly influence grassland ecosystems. This study investigated the spatiotemporal patterns of livestock behaviours under different grazing management systems and grazing-intensity gradients (GIGs) in Wenchang, China, using high-resolution GPS tracking data and machine learning classification. the K-Nearest Neighbours (KNN) model combined with SMOTE-ENN resampling achieved the highest accuracy, with F1-scores of 0.960 and 0.956 for continuous and rotational grazing datasets. The results showed that the continuous grazing system failed to mitigate grazing pressure when grazing intensity was reduced, as the spatial clustering of livestock behaviours did not decrease accordingly, and the frequency of temporal peaks in grazing behaviour even showed an increasing trend. Conversely, the rotational grazing system responded more effectively, as reduced GIGs led to more evenly distributed temporal activity patterns and lower spatial clustering. These findings highlight the importance of incorporating livestock behavioural patterns into grassland monitoring and offer data-driven insights for sustainable grazing management.},
}

Animals
*Machine Learning
*Livestock/physiology
China
Grassland
Spatio-Temporal Analysis
Algorithms
Geographic Information Systems
*Behavior, Animal/physiology
*Herbivory/physiology
Ecosystem

@article {pmid40808268,
year = {2025},
author = {Xu, G and Guo, J and Yu, X and Zhao, N and Li, X and Yuan, T and Xu, Z and Zhao, T and Zhao, S and Li, X and Liu, X},
title = {Multi-Omics Analysis Reveals Adaptive Strategies of Meconopsis horridula to UV-B Radiation in the Qinghai-Tibet Plateau.},
journal = {Plant, cell & environment},
volume = {48},
number = {11},
pages = {8249-8263},
doi = {10.1111/pce.70117},
pmid = {40808268},
issn = {1365-3040},
support = {//This study was supported by the Local Development Funds of the Science and Technology Department of Tibet (Grants XZ202001YD0028C and XZ202102YD0031C), and by the Graduate High-Level Talent Training Program of Tibet University (Grant 2025-GSP-B017)./ ; },
mesh = {*Ultraviolet Rays ; Flavonoids/biosynthesis ; Tibet ; *Adaptation, Physiological ; Transcriptome ; Gene Expression Regulation, Plant ; Altitude ; Arabidopsis/genetics ; Multiomics ; Acyltransferases ; Papaveraceae ; },
abstract = {Meconopsis horridula, an endemic medicinal and alpine horticultural species of the Qinghai-Tibet Plateau, exhibits remarkable adaptation to high-altitude UV-B radiation. Despite its ecological and medicinal significance, the mechanisms underlying its UV-B adaptation remain poorly understood. Here, we used a PacBio full-length transcriptome as a reference, integrating RNA-seq and metabolomic data from altitudinal populations, with field-based transcriptomic and microbiome profiling under shade-controlled UV-B gradients, to elucidate UV-B adaptive regulatory networks. KEGG enrichment and environmental correlation analyses highlighted flavonoid biosynthesis as a central pathway in UV-B adaptation at high altitudes. Controlled UV-B gradient experiments identified 10 conserved flavonoid biosynthesis genes, including chalcone synthase (CHS). Overexpression of CHS in Arabidopsis thaliana increased flavonoid content by approximately 1.2-fold. Co-expression analysis further revealed that CHS-associated regulatory factors mediate coordinated responses, including reduced light signalling, enhanced antioxidant capacity and suppression of defence genes and anthocyanin biosynthesis inhibitors. CHS, in coordination with immune regulation, modulates high-centrality microbes, contributing to differential network regulation and microbiome stability. Enriched key microbes may mitigate the growth-defence trade-off under UV-B stress through antimicrobial, growth-promoting and antioxidant activities. Collectively, our findings reveal a flavonoid-centred adaptation framework that deepens our understanding of UV-B resilience in alpine plants and offers potential resources for crop improvement.},
}

*Ultraviolet Rays
Flavonoids/biosynthesis
Tibet
*Adaptation, Physiological
Transcriptome
Gene Expression Regulation, Plant
Altitude
Arabidopsis/genetics
Multiomics
Acyltransferases
Papaveraceae

@article {pmid40808315,
year = {2025},
author = {Navratilova, HF and Whetton, AD and Geifman, N},
title = {Integrating Food Preference Profiling, Behavior Change Strategies, and Machine Learning for Cardiovascular Disease Prevention in a Personalized Nutrition Digital Health Intervention: Conceptual Pipeline Development and Proof-of-Principle Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e75106},
pmid = {40808315},
issn = {1438-8871},
mesh = {Humans ; *Cardiovascular Diseases/prevention & control ; *Machine Learning ; *Food Preferences ; Female ; Male ; *Precision Medicine ; Middle Aged ; United Kingdom ; Digital Health ; },
abstract = {BACKGROUND: Personalized dietary advice needs to consider the individual's health risks as well as specific food preferences, offering healthier options aligned with personal tastes.

OBJECTIVE: This study aimed to develop a digital health intervention (DHI) that provides personalized nutrition recommendations based on individual food preference profiles (FPP), using data from the UK Biobank.

METHODS: Data from 61,229 UK Biobank participants were used to develop a conceptual pipeline for a DHIs. The pipeline included three steps: (1) developing a simplified food preference profiling tool, (2) creating a cardiovascular disease (CVD) prediction model using the subsequent profiles, and (3) selecting intervention features. The CVD prediction model was created using 3 different predictor sets (Framingham set, diet set, and FPP set) across 4 machine learning models: logistic regression, linear discriminant analysis, random forest, and support vector machine. Intervention functions were designed using the Behavior Change Wheel, and behavior change techniques were selected for the DHI features.

RESULTS: The feature selection process identified 14 food items out of 140 that effectively classify FPPs. The food preference profile prediction set, which did not include blood measurements or detailed nutrient intake, demonstrated comparable accuracy (across the 4 models: 0.721-0.725) to the Framingham set (0.724-0.727) and diet set (0.722-0.725). Linear discriminant analysis was chosen as the best-performing model. Four key features of the DHI were identified: food source and portion information, recipes, a dietary recommendation system, and community exchange platforms. The FPP and CVD risk prediction model serve as inputs for the dietary recommendation system. Two levels of personalized nutrition advice were proposed: level 1-based on food portion intake and FPP; and level 2-based on nutrient intake, FPP, and CVD risk probability.

CONCLUSIONS: This study presents proof of principle for a conceptual pipeline for a DHI that empowers users to make informed dietary choices and reduce CVD risk by catering to person-specific needs and preferences. By making healthy eating more accessible and sustainable, the DHI has the potential to significantly impact public health outcomes.},
}

Humans
*Cardiovascular Diseases/prevention & control
*Machine Learning
*Food Preferences
Female
Male
*Precision Medicine
Middle Aged
United Kingdom
Digital Health

@article {pmid40811794,
year = {2025},
author = {Shen, S and Qi, W and Zeng, J and Li, S and Liu, X and Zhu, X and Dong, C and Wang, B and Shi, Y and Yao, J and Wang, B and Lou, X and Gu, S and Li, P and Wang, J and Jiang, G and Cao, S},
title = {Passive Sensing for Mental Health Monitoring Using Machine Learning With Wearables and Smartphones: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e77066},
pmid = {40811794},
issn = {1438-8871},
mesh = {*Wearable Electronic Devices ; Humans ; *Machine Learning ; *Smartphone ; *Mental Health ; *Mental Disorders/diagnosis ; Monitoring, Physiologic ; },
abstract = {BACKGROUND: Mental health issues have become a significant global public health challenge. Traditional assessments rely on subjective methods with limited ecological validity. Passive sensing via wearable devices and smartphones, combined with machine learning (ML), enables objective, continuous, and noninvasive mental health monitoring.

OBJECTIVE: This study aimed to provide a comprehensive review of the current state of passive sensing-based and ML technologies for mental health monitoring. We summarized the technical approaches, revealed the association patterns between behavioral features and mental disorders, and explored potential directions for future advancements.

METHODS: This scoping review adhered to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews) guidelines and was prospectively registered on the Open Science Framework. We systematically searched 7 databases (Web of Science, PubMed, IEEE Xplore, Embase, PsycINFO, Scopus, and ACM Digital Library) for studies published between January 2015 and February 2025. We included 42 peer-reviewed studies that used passive sensing from wearables or smartphones with ML to monitor clinically diagnosed mental disorders, such as depression and anxiety. Data were synthesized across technical dimensions (data collection, preprocessing, feature engineering, and ML models) and clinical associations, with behavioral features categorized into 8 domains.

RESULTS: The 42 included studies were predominantly cohort designs (23/42, 55%), with a median sample size of 60.5 (IQR 54-99). Most studies focused on depression (23/42, 55%) and anxiety (9/42, 21%) using primarily wrist-worn devices (32/42, 76%) collecting heart rate (28/42, 67%), movement index (25/42, 60%), and step count (17/42, 40%) as key biomarkers. Deep learning models (eg, convolutional neural networks and long short-term memory) showed high accuracy, while traditional ML (eg, random forest) remained prevalent due to better interpretability. We identified critical limitations, including small samples (32/42, 76% with N<100), short monitoring periods (19/42, 45% <7 days), scarce external validation (1/42, 2%), and limited reporting on data anonymization (6/42, 14%).

CONCLUSIONS: While passive sensing and ML demonstrate promising accuracy (eg, convolutional neural network-long short-term memory achieving 92.16% in anxiety detection), the evidence remains constrained by three key limitations: (1) methodological heterogeneity (32/42, 76% single-device studies; 19/42, 45% with <7-day monitoring), (2) high risk of bias from small samples (median 60.5, IQR 54-99 participants) and scarce external validation (1/42, 2%), and (3) ethical gaps (only 6/42, 14% addressing anonymization). These findings underscore the technology's potential to transform mental health care through objective, continuous monitoring-particularly for depression (heart rate and step count biomarkers) and anxiety (sleep and social interaction patterns). However, clinical translation requires standardized protocols, larger longitudinal studies (≥3 months), and ethical frameworks for data privacy. Future work should prioritize multimodal sensor fusion and explainable artificial intelligence to bridge the gap between technical performance and clinical deployability.},
}

*Wearable Electronic Devices
Humans
*Machine Learning
*Smartphone
*Mental Health
*Mental Disorders/diagnosis
Monitoring, Physiologic

@article {pmid40812171,
year = {2025},
author = {Lundberg, DS and Bergelson, J and Roux, F and Weigel, D and Karasov, TL},
title = {Lab to field: Challenges and opportunities for plant biology.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1212-1216},
doi = {10.1016/j.chom.2025.05.027},
pmid = {40812171},
issn = {1934-6069},
mesh = {*Plants/microbiology ; Plant Diseases/microbiology ; *Plant Physiological Phenomena ; },
abstract = {Plant-microbe research offers many choices of model and strain and whether a field-first or lab-first approach is best. However, differences between laboratory studies, offering control and repeatability, versus field experiments, revealing ecological relevance and environmental effects, should not be seen as failure but motivate further inquiry and allow complementary discovery.},
}

*Plants/microbiology
Plant Diseases/microbiology
*Plant Physiological Phenomena

@article {pmid40814786,
year = {2026},
author = {Misono, S and Nguyen-Feng, VN and Lei, X and Feddema, E and Tella, A and Stockness, A and Frazier, PA and Kummerfeld, E and Lim, KO},
title = {Ecological Momentary Assessment of Voice & Psychological Factors: Group & Individual Mechanisms.},
journal = {The Laryngoscope},
volume = {136},
number = {1},
pages = {324-331},
pmid = {40814786},
issn = {1531-4995},
support = {K23DC016335/DC/NIDCD NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1TR002494/TR/NCATS NIH HHS/United States ; KL2 TR000113/TR/NCATS NIH HHS/United States ; K23 DC016335/DC/NIDCD NIH HHS/United States ; KL2TR000113/TR/NCATS NIH HHS/United States ; //American College of Surgeons, Triological Society: Clinical Scientist Development Award/ ; },
mesh = {Humans ; Male ; Female ; Adult ; *Ecological Momentary Assessment ; Middle Aged ; *Dysphonia/psychology/physiopathology ; *Voice Quality ; Cross-Sectional Studies ; Anxiety/psychology ; Stress, Psychological ; Aged ; },
abstract = {OBJECTIVES: Cross-sectional associations between voice and psychological factors are known, but changes over time offer opportunities to refine our understanding of their interactions and consider customized treatment options. Study objectives were to measure relationships between voice and psychological factors using ecological momentary assessment and applying (1) group-level time series analysis and (2) group and (3) individual causal modeling to identify key psychological factors relevant for voice outcomes.

METHODS: Adults (N = 32) with primary muscle tension dysphonia completed multiple assessments daily for 10 days. Measures included items from the Voice Handicap Index-10, voice-adapted perceived present control scale, items from NIH PROMIS and the NIH Toolkit to assess distress, and the Positive and Negative Affect Scale. Group-level time series analysis was conducted using dynamic structural equation modeling; causal analysis utilized the Greedy Fast Causal Inference algorithm.

RESULTS: In group-level time series analyses, neither perceived control nor distress predicted subsequent timepoint voice handicap scores. In group-level causal modeling, anxiety was causal for voice handicap, but perceived control was not. Individual-level analyses identified various causal factors for voice handicap including perceived control and negative affect, and to a lesser extent, serenity, anxiety, somatic arousal, and stress.

CONCLUSIONS: Group-level analyses may obscure important heterogeneity that is identifiable using individual-level causal analyses. For example, perceived control was not identified as predictive or causal for voice handicap at the group level; but was a salient causal factor for voice handicap in some individuals. Causal modeling using intensive longitudinal datasets offers a potential avenue for individualized treatment approaches.},
}

Humans
Male
Female
Adult
*Ecological Momentary Assessment
Middle Aged
*Dysphonia/psychology/physiopathology
*Voice Quality
Cross-Sectional Studies
Anxiety/psychology
Stress, Psychological
Aged

@article {pmid40816181,
year = {2025},
author = {Xu, Z and Xu, D and Ma, J and Wang, J and Yan, S and Fu, R and Cui, Y},
title = {The risk assessment for metal(loid)s in soil-slag mixing systems: Coupling sequential extraction, leaching tests, and in vitro bioaccessibility assays.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139544},
doi = {10.1016/j.jhazmat.2025.139544},
pmid = {40816181},
issn = {1873-3336},
mesh = {Risk Assessment ; *Soil Pollutants/analysis/toxicity ; *Metalloids/analysis/toxicity ; Biological Availability ; Humans ; *Industrial Waste/analysis ; Soil/chemistry ; *Metals, Heavy/analysis ; *Metals/analysis ; Arsenic ; Metallurgy ; },
abstract = {The metals and metalloids (metal[loid]s) in the newly formed soil-slag mixing systems (SSMS), formed by the invasion of smelting slag into contaminated soils, may pose potential risks to environment and residents near the smelter sites. In this study, sequential extraction, leaching tests and in vitro bioaccessibility assays were conducted to assess the ecological and human health risk of metal(loid)s in SSMS. The results indicated that the contaminated soils and smelting slags were composed of more than 80 % silicate and oxide minerals, which served as the host phases for metal(loid)s in SSMS. Cd exhibited high mobility and availability, with its exchangeable fraction ranging from 0.15 % to 69.23 %. Leaching tests revealed high leachability and bioavailability of Cd, Mn and Zn. Moreover, metal(loid)s bioaccessibility varied amongst samples: 2.78-46.63 % of As, 11.87-95.25 % of Cd, 37.35-93.88 % of Mn, 1.97-87.84 % of Pb and 0-57.98 % of Zn. Risk assessment calculation results indicated potentially ecological risks posed by Cd, Mn, Pb, and Zn, and unfavorable carcinogenic risks associated with As and Cd, suggesting that remediation efforts were warranted. Overall, this study highlighted how the invasion of smelting slags can affect the accuracy of risk assessments, providing new guidance for risk control and environmental management at slag dumping sites.},
}

Risk Assessment
*Soil Pollutants/analysis/toxicity
*Metalloids/analysis/toxicity
Biological Availability
Humans
*Industrial Waste/analysis
Soil/chemistry
*Metals, Heavy/analysis
*Metals/analysis
Arsenic
Metallurgy

@article {pmid40817347,
year = {2025},
author = {Rajpal, H and Stengel, CV and Mediano, PAM and Rosas, FE and Viegas, E and Marquet, PA and Jensen, HJ},
title = {Information dynamics and the emergence of high-order individuality in ecosystems.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1231},
pmid = {40817347},
issn = {2399-3642},
support = {EP/W024020/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/X03870X/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/W007142/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; ES/T005319/2//RCUK | Economic and Social Research Council (ESRC)/ ; },
mesh = {*Ecosystem ; *Biological Evolution ; *Selection, Genetic ; Mutation ; Population Dynamics ; *Information Theory ; },
abstract = {At what level does natural selection occur? When considering the reproductive dynamics of interacting and mutating agents, it has long been debated whether selection is better understood by focusing on the individual or if hierarchical selection emerges as a consequence of joint adaptation. Despite longstanding efforts in theoretical ecology, there is still no consensus on this fundamental issue, most likely due to the difficulty in obtaining adequate data spanning a sufficient number of generations and the lack of adequate tools to quantify the effect of hierarchical selection. Here, we capitalise on recent advances in information-theoretic data analysis to advance this state of affairs by investigating the emergence of high-order structures- such as groups of species- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that evolutionary dynamics can lead to clusters of species that act as a self-perpetuating group that exhibits greater information-theoretic agency than a single species for a broad range of stable mutation rates. However, this higher-order organization breaks down for mutation rates close to the error threshold, where increased information processing is observed at the level of a single species. For mutation rates higher than the error threshold, no stable population of species are observed in time, and all individuality is lost in the ecosystem. Overall, our findings provide quantitative evidence supporting the emergence of higher-order structures in evolutionary ecology from relatively simple processes of adaptation and reproduction.},
}

*Ecosystem
*Biological Evolution
*Selection, Genetic
Mutation
Population Dynamics
*Information Theory

@article {pmid40818234,
year = {2025},
author = {Poudel, B and Xie, J and Guo, C and Watt, OE and Pulster, EL and Patel, RJ and Steevens, JA and Xu, D},
title = {Real-time oil spill concentration assessment through fluorescence imaging and deep learning.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139374},
doi = {10.1016/j.jhazmat.2025.139374},
pmid = {40818234},
issn = {1873-3336},
abstract = {Oil spills may pose severe ecological and socioeconomic threats, necessitating rapid and accurate environmental assessment. Traditional assessment methods used to determine the extent of a spill including gas chromatography-mass spectrometry, satellite imaging, and visual surveys, are often time-consuming, expensive, and limited by weather conditions or sampling constraints. Furthermore, these methods frequently struggle to provide real-time data crucial for prompt decision-making during spill emergencies. This study addresses these limitations by combining fluorescence imaging, deep learning, a mobile application, and a data management system for automated and real-time oil spill assessment. Our approach leverages a convolutional neural network architecture for feature extraction coupled with a custom regression model, trained and evaluated on a self-curated comprehensive dataset of 1530 fluorescence images from two distinct oil types, a napthalenic crude oil and an aromatic-napthalenic crude oil, at concentrations ranging from 0 to 500 mg/L. The proposed approach demonstrates superior performance compared to both traditional machine learning models and more complex deep learning architectures, achieving an R[2] score of 0.9958 and RMSE of 9.28. The application enables rapid, cost-effective field measurements with robust data tracking and analysis capabilities. This research advances oil spill monitoring technology with a scalable solution that balances accuracy, speed, and accessibility for real-time environmental assessment and emergency response.},
}

@article {pmid40819189,
year = {2025},
author = {Alhashmi, AA and Elhessewi, GMS and Ghaleb, M and Ahmad, N and Aljehane, NO and Alkhaldi, TM and Almansour, H and Al Zanin, S},
title = {Enhancing medical response efficiency in real-time large crowd environments via smart coverage and deep learning for stable ecological health monitoring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30000},
pmid = {40819189},
issn = {2045-2322},
mesh = {*Deep Learning ; Humans ; Geographic Information Systems ; *Crowding ; Algorithms ; },
abstract = {Festivals and city-wide mass events are prevalent in human societies worldwide, drawing large crowds. Such events range from concerts with a dozen attendees to large-scale actions with thousands of viewers. It is the highest priority for each organizer of such an occasion to be capable of upholding a higher standard of safety and minimizing the danger of events, especially medical emergencies. Therefore, establishing sufficient safety measures is significant. There is a requirement for event organizers and emergency response personnel to identify developing, potentially critical crowd situations at an early stage during city-wide mass assemblies. In general, the localization of the global positioning system (GPS) and proximity-based tracking is employed to capture intricate crowd dynamics throughout an event. Recently, technology has been used in numerous diverse ways to achieve these large crowds. For example, computer vision-based models are employed to observe the flexibility and behaviour of crowds. In this manuscript, a model for Medical Response Efficiency in Real-Time Large Crowd Environments via Smart Coverage and Hiking Optimisation (MRELC-SCHO) is presented, aiming to maintain stable ecological health. The primary objective of this paper is to propose an effective method for enhancing medical response efficiency in large crowd environments by utilizing advanced optimization algorithms. Initially, the MRELC-SCHO model utilizes min-max normalization to transform the input data into a structured format. Furthermore, the Chimp Optimisation Algorithm (CHOA) model is employed for the feature selection (FS) process to select the most significant features from the dataset. Additionally, the MRELC-SCHO technique utilizes the bidirectional long short-term memory with an auto-encoder (BiLSTM-AE) method for classification. Finally, the parameter selection for the BiLSTM-AE model is performed by using the Hiking Optimisation Algorithm (HOA) model. The experimentation of the MRELC-SCHO approach is accomplished under the Ecological Health dataset. The comparison analysis of the MRELC-SCHO approach revealed a superior accuracy value of 98.56% compared to existing models.},
}

*Deep Learning
Humans
Geographic Information Systems
*Crowding
Algorithms

@article {pmid40820130,
year = {2025},
author = {Sehi, GT and Birhanie, SK and Hans, J and Brown, MQ and Parker, DM},
title = {Environmental correlates of Aedes aegypti abundance in the West Valley region of San Bernardino County, California, USA, from 2017 to 2023: an ecological modeling study.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {349},
pmid = {40820130},
issn = {1756-3305},
support = {U01 CK000649/CK/NCEZID CDC HHS/United States ; U01CK000649/ACL/ACL HHS/United States ; },
mesh = {Animals ; *Aedes/physiology/virology ; California/epidemiology ; *Mosquito Vectors/physiology/virology ; Geographic Information Systems ; Temperature ; *Environment ; Ecosystem ; Dengue/transmission ; Mosquito Control ; Humans ; },
abstract = {BACKGROUND: Aedes mosquitoes, particularly Aedes aegypti and Ae. albopictus, are major vectors of globally significant diseases such as dengue, Zika, and chikungunya. Since 2013, Ae. aegypti populations have rapidly expanded in California, making control efforts difficult due to their widespread, small-scale breeding sites and strong adaptation to urban environments.

METHODS: Remote sensing technologies, coupled with Geographic Information Systems (GIS), offer innovative solutions for mosquito surveillance and control. However, understanding the environmental drivers of mosquito abundance, particularly in California's diverse ecological settings, remains an important gap. To address this gap, we analyzed Ae. aegypti abundance (2017 to 2023) in relation to environmental variables, such as temperature, precipitation, surface water, elevation, and built environment. We applied hotspot analysis to identify spatial clusters of high mosquito abundance and used a generalized additive model (GAM) with a negative binomial distribution to assess environmental and meteorological influences on mosquito counts.

RESULTS: Hotspot analyses revealed clusters of Ae. aegypti hotspots near residential areas. Aedes aegypti counts increased with higher surface water availability and temperature.

CONCLUSIONS: Our study characterizes the spatial and temporal dynamics of Ae. aegypti mosquito abundance in the West Valley region of San Bernardino County from 2017 to 2023, shedding light on the influence of environmental factors and human activities on temporal trends. Our findings emphasize the critical role of temperature and water availability in shaping mosquito population dynamics, highlighting the need for proactive vector control strategies in response to environmental changes.},
}

Animals
*Aedes/physiology/virology
California/epidemiology
*Mosquito Vectors/physiology/virology
Geographic Information Systems
Temperature
*Environment
Ecosystem
Dengue/transmission
Mosquito Control
Humans

@article {pmid40820776,
year = {2025},
author = {Stansberry, TT and Myers, CR and Tran, L and Roberson, PNE and Ahn, S},
title = {Impacts of Access to Hospital and Emergency Care on Rural Mortality in Tennessee, 2010-2019: A GIS-Informed Study.},
journal = {Journal of health care for the poor and underserved},
volume = {36},
number = {3},
pages = {787-814},
doi = {10.1353/hpu.2025.a967333},
pmid = {40820776},
issn = {1548-6869},
mesh = {Humans ; Tennessee/epidemiology ; *Health Services Accessibility/statistics & numerical data ; Retrospective Studies ; *Rural Population/statistics & numerical data ; Cross-Sectional Studies ; Middle Aged ; Geographic Information Systems ; Female ; Male ; COVID-19/epidemiology ; Adult ; Aged ; *Mortality/trends ; *Emergency Medical Services/statistics & numerical data ; },
abstract = {Rural Tennessee's health and economic disparities have worsened since 2010 (while the state led the nation in hospital closures per capita). Guided by the Vulnerable Populations Conceptual Model, we examined the relationship between Tennessee's county-level rural mortality rates and declining access to hospital and emergency care in the decade preceding the COVID-19 pandemic (avoiding pandemic-related delayed data releases and potential statistical modeling issues). We conducted a retrospective, ecological correlational study using geographic information systems and annual cross-sectional secondary data, employing aspatial and spatial negative binomial generalized linear mixed-effects models (GLMMs). Our bivariate models revealed significant correlations between hospital and emergency care access and mortality rates, but the effect decreased when adjusted for rurality, median household income, age, and other covariates. While access to hospital and emergency care influences mortality, our findings indicate that socioeconomic and demographic factors have a greater impact, underscoring the strong health-wealth connection in rural Tennessee.},
}

Humans
Tennessee/epidemiology
*Health Services Accessibility/statistics & numerical data
Retrospective Studies
*Rural Population/statistics & numerical data
Cross-Sectional Studies
Middle Aged
Geographic Information Systems
Female
Male
COVID-19/epidemiology
Adult
Aged
*Mortality/trends
*Emergency Medical Services/statistics & numerical data

@article {pmid40821442,
year = {2025},
author = {Motlagh, SH and Momtazi, F and Saeedi, H},
title = {Senckenberg dogger bank long-term monitoring: First dataset on amphipods.},
journal = {Data in brief},
volume = {62},
number = {},
pages = {111931},
pmid = {40821442},
issn = {2352-3409},
abstract = {This dataset includes unique occurrence records of amphipod specimens collected during the 2024 annual Senckenberg Long-Term Monitoring Project in Dogger Bank (a shallow sand bank in the central North Sea), Cruise DOG24. This cruise was part of an ongoing effort to monitor biodiversity, which has occurred annually from 1991 to 2024 by the Marine Zoology Department at the Senckenberg Research Institute and Natural History Museum. Amphipods, key components of marine benthic ecosystems, were sampled by beam trawl over the Dogger Bank's stable sandy substrate. A total of 8444 specimens of ten species belonging to 13 families and 14 genera were identified using morphological methods with Leica M60 and DM750 microscopes. This study presents the first species-level identification of benthic amphipods in the Dagger Bank, providing a taxonomically resolved dataset that serves as a reliable identification key for future monitoring efforts in the area. Data were structured and published to the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF) following the Darwin Core (DwC) standard. This dataset is the first-hand data ever published open-access from the Senckenberg Long Term Monitoring Project since 1991. This dataset also supports a broader research project aimed at (i) revealing the distribution pattern of amphipods in the North Sea, (ii) identifying environmental drivers of species distribution and diversity, and (iii) evaluating the response of the amphipod community to ecosystem changes.},
}

@article {pmid40822726,
year = {2025},
author = {Piršelová, B and Jakubčinová, J},
title = {Plant cyanogenic glycosides: from structure to properties and potential applications.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1612132},
pmid = {40822726},
issn = {1664-462X},
abstract = {Cyanogenic glycosides (CGs) represent an important group of secondary metabolites predominantly of plant origin, characterized by their ability to release hydrogen cyanide upon enzymatic hydrolysis. These compounds are widely distributed across the plant kingdom, where they play a crucial role in defense against herbivores and pathogens. In recent years, advanced analytical tools have greatly expanded our knowledge of CGs by enabling the identification of less abundant forms. Based on the latest data from published scientific studies, this review presents a comprehensive overview of CGs, with a focus on their structural variability, biosynthetic pathways, ecological functions, and inherent toxicity. Special attention is given to the quantity and distribution of significant CGs in plants, as the available data is often heterogeneous, fragmented, and dispersed across the literature. Furthermore, the review explores emerging evidence regarding the biomedical relevance of selected CGs, including their putative anticancer properties and broader therapeutic potential. The findings presented in this review may be applied in fields such as pharmacology, toxicology, food safety, and plant biotechnology - either to enhance CG content for crop protection or, conversely, to eliminate such content in order to improve food safety.},
}

@article {pmid40824055,
year = {2025},
author = {Grigson, SR and Bouras, G and Dutilh, BE and Olson, RD and Edwards, RA},
title = {Computational function prediction of bacteria and phage proteins.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {89},
number = {3},
pages = {e0002225},
pmid = {40824055},
issn = {1098-5557},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; 865694/ERC_/European Research Council/International ; RC2DK116713/DK/NIDDK NIH HHS/United States ; 390713860//Deutsche Forschungsgemeinschaft/ ; DP220102915//Australian Research Council/ ; FL250100019//Australian Research Council/ ; },
mesh = {*Bacteriophages/genetics/metabolism ; *Computational Biology/methods ; *Viral Proteins/genetics/metabolism/chemistry ; *Bacteria/genetics/metabolism ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; Molecular Sequence Annotation/methods ; },
abstract = {SUMMARYUnderstanding protein functions is crucial for interpreting microbial life; however, reliable function annotation remains a major challenge in computational biology. Despite significant advances in bioinformatics methods, ~30% of all bacterial and ~65% of all bacteriophage (phage) protein sequences cannot be confidently annotated. In this review, we examine state-of-the-art bioinformatics tools and methodologies for annotating bacterial and phage proteins, particularly those of unknown or poorly characterized function. We describe the process of identifying protein-coding regions and the systems to classify protein functionalities. Additionally, we explore a range of protein annotation methods, from traditional homology-based methods to cutting-edge machine learning models. In doing so, we provide a toolbox for confidently annotating previously unknown bacterial and phage proteins, advancing the discovery of novel functions and our understanding of microbial systems.},
}

*Bacteriophages/genetics/metabolism
*Computational Biology/methods
*Viral Proteins/genetics/metabolism/chemistry
*Bacteria/genetics/metabolism
*Bacterial Proteins/genetics/metabolism/chemistry
Machine Learning
Molecular Sequence Annotation/methods

@article {pmid40825407,
year = {2025},
author = {Tarandek, A and Boštjančić, LL and Francesconi, C and Bonassin, L and Schardt, L and Jussila, J and Kokko, H and Schwenk, K and Hudina, S and Lecompte, O and Theissinger, K},
title = {Characterisation of the noble crayfish immune response to oomycete-derived immunostimulants.},
journal = {Fish & shellfish immunology},
volume = {166},
number = {},
pages = {110666},
doi = {10.1016/j.fsi.2025.110666},
pmid = {40825407},
issn = {1095-9947},
mesh = {Animals ; *Astacoidea/immunology/genetics/microbiology ; *Aphanomyces/chemistry/physiology/immunology ; *Adjuvants, Immunologic/pharmacology ; *Glucans/pharmacology ; *Immunity, Innate ; Hemocytes/immunology ; },
abstract = {The invasive oomycete pathogen Aphanomyces astaci significantly threatens native European crayfish populations, prompting investigations towards the effects of protective immunostimulation on the immune response of the vulnerable noble crayfish (Astacus astacus). Here, we evaluate the effect of three oomycete-derived immunostimulant treatments: laminarin (β-1,3-glucan found within the Ap. astaci cell wall), inactivated Ap. astaci spores and Ap. astaci hyphal homogenate. Our findings reveal immediate changes in the noble crayfish total haemocyte count (THC), differential haemocyte count (DHC), and gene expression. A short-term increase in the THC was observed in all treatments, with a gradual return to normal values 8 h post immunostimulation. Granular haemocytes seem to be involved in response to immunostimulation with inactivated Ap. astaci spores, while the number of semi-granular and hyaline haemocytes increased in response to laminarin and Ap. astaci hyphal homogenate. Analysis of the differentially expressed genes showed that the Prophenoloxidase pathway genes and Toll pathway genes are involved in the response to oomycete-derived immunostimulants. Prolonged effects of immunostimulation were reflected in the decreased C/EBP and Kr-h1 gene expression in the hyphal homogenate group as well as decreased Kr-h1 expression in the spore group. Taken together, our results indicate that immunostimulation causes a dynamic change in the noble crayfish immune system response, with similarities in the gene expression patterns between immunostimulated and Ap. astaci infected noble crayfish. As a future research focus, we highlight the importance of molecular characterisation of the genes involved in the anti-oomycete response which could provide valuable insights into pathogen resistance in freshwater crayfish. In the context of the Ap. astaci mediated downfall of the noble crayfish stocks across Europe, further exploration is needed regarding the benefits of the oomycete-derived immunostimulation that can potentially support conservation and aquacultural efforts.},
}

Animals
*Astacoidea/immunology/genetics/microbiology
*Aphanomyces/chemistry/physiology/immunology
*Adjuvants, Immunologic/pharmacology
*Glucans/pharmacology
*Immunity, Innate
Hemocytes/immunology

@article {pmid40826054,
year = {2025},
author = {Quintanilha, D and Moura, E and Xavier, D},
title = {Hospitalisations in Brazil: an ecological time series analysis of the impact of medical decision support data as an exogenous variable.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {2827},
pmid = {40826054},
issn = {1471-2458},
mesh = {Brazil/epidemiology ; Humans ; *Hospitalization/statistics & numerical data ; *Decision Support Systems, Clinical/statistics & numerical data ; *Public Health Surveillance/methods ; },
abstract = {PURPOSE: Public health surveillance depends on continuous monitoring to guide interventions and allocate resources effectively. This study aimed to evaluate whether structured medical search data from the Afya Whitebook®, a clinical decision-support platform, can serve as exogenous variables to enhance the explanatory capacity of time series models characterising hospitalisation patterns within Brazil's public health system.

METHODS: An ecological time series analysis was conducted using hospitalisation data (SIH/SUS) and Afya Whitebook® search volumes from 2021 to 2024. SARIMAX models assessed temporal associations between search activity and hospital admissions across Brazilian states, compared to univariate SARIMA models to evaluate the added value of search data.

RESULTS: In 278 of the 478 time series, SARIMAX models provided a better fit than univariate SARIMA models, particularly for conditions such as chronic obstructive pulmonary disease, dengue, urinary tract infections, type 2 diabetes, asthma, depression, and chronic kidney disease. Model fit varied by disease and region, underscoring the influence of contextual factors in the association between search behaviour and hospital admissions.

CONCLUSION: This study demonstrates that structured medical search data can serve as exogenous variables to improve the explanatory capacity of time series models of hospitalisation patterns. Despite variation between diseases and regions, this approach shows promise in supporting public health surveillance and could be strengthened by incorporating contextual data in future studies.},
}

Brazil/epidemiology
Humans
*Hospitalization/statistics & numerical data
*Decision Support Systems, Clinical/statistics & numerical data
*Public Health Surveillance/methods

@article {pmid40827702,
year = {2025},
author = {Chung, J and Moloney, ME and Seixas, AA and Jackson, CL},
title = {The environment around the sleeper is changing: a perspective.},
journal = {Sleep},
volume = {48},
number = {11},
pages = {},
pmid = {40827702},
issn = {1550-9109},
support = {5R01HL152453-05/GF/NIH HHS/United States ; },
mesh = {Humans ; *Sleep/physiology ; Weather ; *Environmental Exposure/adverse effects ; *Environment ; Circadian Rhythm/physiology ; Temperature ; },
abstract = {Sleep is shaped by a complex interplay of biological, behavioral, and environmental factors. While substantial attention has been paid to the first two factors, the role of environmental exposures, particularly weather patterns, ambient temperature variability, and other dynamic atmospheric conditions, remains relatively underexplored in sleep research. This gap is notable given the increasing availability of high-resolution environmental data and growing evidence that ambient conditions can influence circadian regulation, thermal comfort, and sleep continuity. This perspective paper reviews emerging evidence linking environmental factors to sleep patterns, highlighting both direct effects (e.g. thermal disruptions) and indirect pathways (e.g., displacement or stress from extreme weather events). Recent advances in environmental sensing, geospatial data, and real-time monitoring offer new opportunities to capture high-resolution environmental data relevant to sleep. This perspective highlights the need for data infrastructure capable of integrating these dynamic environmental inputs with sleep metrics from, for instance, wearables, surveys, and clinical records. We also examine the methodological and informatics challenges of integrating environmental data with sleep measures and suggest directions for future research. As environmental conditions evolve, understanding their influence on sleep holds promise for advancing both scientific knowledge and public health relevance, particularly in identifying affected populations, designing responsive interventions, and contextualizing sleep within broader ecological systems.},
}

Humans
*Sleep/physiology
Weather
*Environmental Exposure/adverse effects
*Environment
Circadian Rhythm/physiology
Temperature

@article {pmid40828274,
year = {2025},
author = {Ramos-Onsins, SE and Guirao-Rico, S and Hafez, A and Ferretti, L},
title = {npstat: An Efficient Tool to Explore the Population Genome Variability and Divergence Using Pool Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {51-66},
pmid = {40828274},
issn = {1940-6029},
mesh = {*Software ; *Genetic Variation ; *Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Computational Biology/methods ; },
abstract = {Pool sequencing has emerged as a valuable approach in ecological studies, particularly when dealing with very small organisms (with limited amount of DNA available), when distinguishing individual organisms is a challenge (e.g., in colonies, microbiome), when there is a trade-off between the sequencing cost and the number of individuals to sequence, when the main goal is to estimate nucleotide variability and variant frequency patterns at the population level (that is, when individual information is not required). Estimates of variability can be efficiently explored by analyzing sequences of pooled individuals sampled from the population. When using this approach, the number of pooled individuals and the mean read depth are key choices in the experimental design.The software npstat calculates different estimates of nucleotide variability and neutrality tests.It also calculates the number of synonymous and nonsynonymous variants and the proportion of beneficial substitutions (alpha) using the MKT approach when GTF annotation file and an outgroup is provided.},
}

*Software
*Genetic Variation
*Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
*Genetics, Population/methods
*Computational Biology/methods

@article {pmid40828279,
year = {2025},
author = {Vizueta, J and Pisarenco, VA and Rozas, J},
title = {Evolutionary Genomics of Gene Families: A Case Study of Insect Gustatory Receptors.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {179-209},
pmid = {40828279},
issn = {1940-6029},
mesh = {Animals ; *Genomics/methods ; *Evolution, Molecular ; *Multigene Family ; Phylogeny ; *Receptors, Cell Surface/genetics ; *Ants/genetics ; Computational Biology/methods ; *Insect Proteins/genetics ; Molecular Sequence Annotation ; },
abstract = {Gene families, which are groups of genes that share common ancestry and are often functionally related, constitute a substantial proportion of the protein-coding sequences within eukaryotic genomes. In insects, genes involved in chemoperception belong to gene families characterized by numerous copies that arise from episodic bursts of gene duplication. This biological process is crucial for insect survival, as it enables the perception of environmental chemical cues. In this chapter, we analyze the gustatory receptors in the fire ant Solenopsis invicta and present a protocol for bioinformatic analyses. First, we employ BITACORA to identify and annotate gene family members in the genome assembly, providing tools for the annotation and subsequent validation. Then, we use GALEON to explore the genomic arrangement of gene family members in the chromosome-level assembly and visualize the distribution of gene clusters. To gain insights into the evolution and function of these genes, we conduct multiple-sequence alignment and reconstruct the phylogeny, incorporating data from two other insects. Finally, we integrate physical and evolutionary distances of the gustatory receptors to further understand the dynamics of this gene family.},
}

Animals
*Genomics/methods
*Evolution, Molecular
*Multigene Family
Phylogeny
*Receptors, Cell Surface/genetics
*Ants/genetics
Computational Biology/methods
*Insect Proteins/genetics
Molecular Sequence Annotation

@article {pmid40828283,
year = {2025},
author = {Aceto, S and Perrini, S and Varone, M and Lucibelli, F and Volpe, G and Di Lillo, P and Carfora, A and Mazzucchiello, SM and Saccone, G and Salvemini, M},
title = {Identification of Sex-Specific and Sex-Biased Transcripts for Genetic Sexing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {273-298},
pmid = {40828283},
issn = {1940-6029},
mesh = {Animals ; Male ; Female ; *Computational Biology/methods ; *Sex Determination Analysis/methods ; *Transcriptome ; },
abstract = {Sex-specific transcripts are RNA molecules expressed predominantly or exclusively in one sex, providing insights into molecular and physiological differences between males and females. This knowledge underpins the development of precise and efficient genetic sexing methods applicable in various contexts. In agriculture and livestock management, early sex determination could enhance resource management and productivity. In ecology and conservation, genetic sexing informs population monitoring and species management. In applied entomology, it could improve biological control strategies, such as the sterile insect technique. Here, we describe a bioinformatic framework to identify sex-specific transcripts using RNA-seq sequencing data in eukaryotic species with or without a sequenced reference genome.},
}

Animals
Male
Female
*Computational Biology/methods
*Sex Determination Analysis/methods
*Transcriptome

@article {pmid40828862,
year = {2025},
author = {Kubota, Y and Fukiage, T},
title = {Human-like monocular depth biases in deep neural networks.},
journal = {PLoS computational biology},
volume = {21},
number = {8},
pages = {e1013020},
pmid = {40828862},
issn = {1553-7358},
mesh = {Humans ; *Neural Networks, Computer ; *Depth Perception/physiology ; *Vision, Monocular/physiology ; Computational Biology ; Male ; Female ; Adult ; },
abstract = {Human depth perception from 2D images is systematically distorted, yet the nature of these distortions is not fully understood. By examining error patterns in depth estimation for both humans and deep neural networks (DNNs), which have shown remarkable abilities in monocular depth estimation, we can gain insights into constructing functional models of this human 3D vision and designing artificial models with improved interpretability. Here, we propose a comprehensive human-DNN comparison framework for a monocular depth judgment task. Using a novel human-annotated dataset of natural indoor scenes and a systematic analysis of absolute depth judgments, we investigate error patterns in both humans and DNNs. Employing exponential-affine fitting, we decompose depth estimation errors into depth compression, per-image affine transformations (including scaling, shearing, and translation), and residual errors. Our analysis reveals that human depth judgments exhibit systematic and consistent biases, including depth compression, a vertical bias (perceiving objects in the lower visual field as closer), and consistent per-image affine distortions across participants. Intriguingly, we find that DNNs with higher accuracy partially recapitulate these human biases, demonstrating greater similarity in affine parameters and residual error patterns. This suggests that these seemingly suboptimal human biases may reflect efficient, ecologically adapted strategies for depth inference from inherently ambiguous monocular images. However, while DNNs capture metric-level residual error patterns similar to humans, they fail to reproduce human-level accuracy in ordinal depth perception within the affine-invariant space. These findings underscore the importance of evaluating error patterns beyond raw accuracy, providing new insights into how humans and computational models resolve depth ambiguity. Our dataset and methodology provide a framework for evaluating the alignment between computational models and human perceptual biases, thereby advancing our understanding of visual space representation and guiding the development of models that more faithfully capture human depth perception.},
}

Humans
*Neural Networks, Computer
*Depth Perception/physiology
*Vision, Monocular/physiology
Computational Biology
Male
Female
Adult

@article {pmid40828878,
year = {2025},
author = {Fong, LJM and Johnson, BD and Darolti, I and Sandkam, BA and Mank, JE},
title = {Genome report: Genome of the Amazon guppy (Poecilia bifurca) reveals conservation of sex chromosomes and dosage compensation.},
journal = {G3 (Bethesda, Md.)},
volume = {15},
number = {10},
pages = {},
pmid = {40828878},
issn = {2160-1836},
support = {//NSERC/ ; //UBC/ ; //BRC Informatics/ ; },
mesh = {Animals ; *Poecilia/genetics ; *Dosage Compensation, Genetic ; Male ; Female ; *Sex Chromosomes/genetics ; *Genome ; *Genomics/methods ; X Chromosome/genetics ; },
abstract = {The Amazon guppy, Poecilia bifurca, is a small live-bearing fish. The close relatives Poecilia reticulata, Poecilia picta, and Poecilia parae all share the same sex chromosome system, but with substantial diversity in the degree of Y degeneration and the extent of X chromosome dosage compensation. In order to identify if P. bifurca shares the same sex chromosome system, we built a female (XX) draft genome with 55X coverage of PacBio HiFi data, resulting in a 785 Mb assembly with 94.4% BUSCO completeness. We used this genome and found that P. bifurca shares the same sex chromosomes as related species and shows substantial Y chromosome degeneration. We combined this with RNA-Seq data and found similar expression of X-linked genes between sexes, revealing that P. bifurca also exhibits complete X chromosome dosage compensation. We further identify 11 putative autosome-to-Y gene duplications, 5 of which show gene expression in guppy male germ cells.},
}

Animals
*Poecilia/genetics
*Dosage Compensation, Genetic
Male
Female
*Sex Chromosomes/genetics
*Genome
*Genomics/methods
X Chromosome/genetics

@article {pmid40829560,
year = {2025},
author = {McKnight, JC and Solms, B and Jensen, M and Turnbull, J and Balfour, S and Laagland, M and Bronkhorst, M and Lee, HJ and Kang, G and Lee, JY and Bell, A and Hastie, G and Ilardo, M},
title = {Diving behaviour and physiology of the Korean Haenyeo.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R797-R798},
doi = {10.1016/j.cub.2025.06.066},
pmid = {40829560},
issn = {1879-0445},
mesh = {Adult ; Female ; Humans ; *Diving/physiology ; Republic of Korea ; *Breath Holding ; },
abstract = {There is a long history of breath-hold diving cultures in East Asia, with references in Japanese chronicles as early as the third century BC. Given evidence of genetic adaptations for phenotypes associated with enhanced diving capacity within such populations[1], it is likely they hold the most prodigious human diving abilities - abilities that may be akin to semi-aquatic mammals, and even some marine mammals. Yet, a dearth of fine-scale information exists on the combined natural diving behaviour and physiological responses within these diving populations. One such extraordinary population is the all-female Haenyeo. Here, we assess the fine-scale diving behaviours and physiological responses of these women during natural harvest diving. Our results show that Haenyeo divers demonstrate the highest proportions of time underwater of any humans, also exceeding those of semi-aquatic mammals and being comparable with some marine mammals. Additionally, they do not exhibit an overt cardiovascular depression, or 'dive response', classically associated with consummate diving mammals.},
}

Adult
Female
Humans
*Diving/physiology
Republic of Korea
*Breath Holding

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

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

@article {pmid40838167,
year = {2025},
author = {Boyes, D and Fletcher, C and Phillips, D and Sivess, L and Boyes, C and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Tortix moth, Archips podanus (Scopoli, 1763).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {189},
pmid = {40838167},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Archips podanus (Tortix moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence has a total length of 549.00 megabases. Most of the assembly (99.72%) is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.45 kilobases.},
}

@article {pmid40840423,
year = {2025},
author = {Bozeman, BB and Matson, PG and DeRolph, CR and DeNeale, ST},
title = {The HydroBio Dataset: a new data resource for evaluating existing and potential hydropower capacity and freshwater biodiversity in the conterminous United States.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127042},
doi = {10.1016/j.jenvman.2025.127042},
pmid = {40840423},
issn = {1095-8630},
mesh = {*Biodiversity ; Conservation of Natural Resources ; Ecosystem ; *Fresh Water ; *Power Plants ; Rivers ; United States ; *Datasets as Topic ; },
abstract = {Hydropower is a critical source of affordable and reliable electricity and energy system stability services in the United States. Opportunities to expand US hydropower production include retrofitting existing non-powered dams to produce power, retrofitting existing hydropower dams to improve efficiency or increase capacity, or constructing new hydropower infrastructure on currently unregulated river reaches. We created the HydroBio Dataset, which summarizes existing and potential hydropower capacity and freshwater biodiversity at the sub-basin scale in the conterminous US to contextualize existing and potential grid contributions with the freshwater ecosystems in which dams are situated. We demonstrate a use-case of this dataset by rescaling and comparing potential non-powered dam nominal capacity to rarity-threat-weighted freshwater species richness for sub-basins where both types of data exist. On average, normalized freshwater biodiversity exceeded normalized potential non-powered dam nominal capacity in these sub-basins. Potential non-powered dam nominal capacity was concentrated in sub-basins in the Upper Mississippi and Ohio hydrologic regions while freshwater biodiversity was concentrated in the South Atlantic-Gulf, Ohio, and Tennessee hydrologic regions. Additionally, non-powered dams and existing hydropower dams are located in sub-basins with similar indices of freshwater biodiversity. The HydroBio Dataset adds an additional ecological dimension of context to our understanding of current and potential future US hydropower capabilities and is a valuable decision support tool for stakeholders tasked with balancing gains in services to the US power grid with the public and environmental benefits of freshwater ecosystems.},
}

*Biodiversity
Conservation of Natural Resources
Ecosystem
*Fresh Water
*Power Plants
Rivers
United States
*Datasets as Topic

@article {pmid40840460,
year = {2025},
author = {Carlozzi, NE and Troost, J and Lombard, WL and Miner, JA and Graves, CM and Choi, SW and Wu, Z and Sen, S and Sander, AM},
title = {Completion and Compliance Rates for an Intensive mHealth Study Design to Promote Self-Awareness and Self-Care Among Care Partners of Individuals With Traumatic Brain Injury: Secondary Analysis of a Randomized Controlled Trial.},
journal = {JMIR mHealth and uHealth},
volume = {13},
number = {},
pages = {e73772},
pmid = {40840460},
issn = {2291-5222},
support = {K24 HL156896/HL/NHLBI NIH HHS/United States ; R01 HL146354/HL/NHLBI NIH HHS/United States ; R01 NR013658/NR/NINR NIH HHS/United States ; UL1 TR002240/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Awareness ; *Brain Injuries, Traumatic/psychology/therapy ; *Caregivers/psychology/statistics & numerical data ; Mobile Applications/statistics & numerical data/standards ; *Patient Compliance/statistics & numerical data/psychology ; *Self Care/methods/psychology/standards/statistics & numerical data ; Surveys and Questionnaires ; Telemedicine/standards/statistics & numerical data ; *Treatment Adherence and Compliance/statistics & numerical data/psychology ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Compliance rates for mobile health (mHealth) studies that involve intensive study designs are highly variable. Both person- and study-specific factors likely contribute to this variability. We were interested in understanding the impact that care partner characteristics and demographics have on study engagement, given that engagement is critical to the success of mHealth interventions.

OBJECTIVE: The primary objective of this report was to analyze the overall and component-specific completion and compliance rates for an intensive 6-month mHealth intervention (CareQOL app) designed to promote self-awareness and self-care among care partners of individuals with traumatic brain injury.

METHODS: This randomized controlled trial was designed to test the CareQOL app, an mHealth app designed to promote care partner self-awareness (through self-monitoring) and self-care (through personalized self-care push notifications). The study design consisted of a baseline assessment, a 6-month home-monitoring period that included 3 daily ecological momentary assessment (EMA) questions, monthly patient-reported outcome (PRO) surveys, continuous activity and sleep monitoring using a Fitbit, and 2 follow-up PRO surveys at 3 and 6 months posthome monitoring. Three participants withdrew prior to the initiation of the home-monitoring period, resulting in a final analytical sample size of 254. All participants had access to a self-monitoring dashboard (CareQOL app) that included graphical displays of the daily survey scores, as well as daily steps and sleep data from the Fitbit.

RESULTS: Overall compliance for the different aspects of the study was high. On average, the full-sample daily EMA PRO completion rate was 84% (SD 19%), Fitbit-based step count compliance was 90% (SD 21%), and Fitbit-based sleep duration compliance was 75% (SD 32%); there was no difference between the study arms for daily EMA PROs and Fitbit compliance rates. Completion rates for monthly and follow-up PRO surveys were even higher, with average end-of-month completion rates ranging from 97% to 100%, and follow-up completion rates of 95% for both time points. Again, these rates did not differ by study arm. The data were represented by 3 engagement groups: high-compliance-all data; high-compliance-PROs and steps only; and moderate PRO compliance-low Fitbit compliance. Group membership was predicted by both race (P<.001) and relationship to the care recipient (P=.001), but not by the other person-specific variables.

CONCLUSIONS: The compliance rates for this intensive study design are consistent, but at the high end, with what has been reported previously in the literature for studies with shorter time durations. Except for race and relationship to the care recipient, person-specific factors did not appear to be significantly associated with the engagement group. As such, we anticipate that the high compliance rates observed in this study are likely due to several study-specific design elements that were used to encourage study engagement.},
}

Adult
Female
Humans
Male
Middle Aged
*Awareness
*Brain Injuries, Traumatic/psychology/therapy
*Caregivers/psychology/statistics & numerical data
Mobile Applications/statistics & numerical data/standards
*Patient Compliance/statistics & numerical data/psychology
*Self Care/methods/psychology/standards/statistics & numerical data
Surveys and Questionnaires
Telemedicine/standards/statistics & numerical data
*Treatment Adherence and Compliance/statistics & numerical data/psychology
Secondary Data Analysis

@article {pmid40840863,
year = {2025},
author = {Zong, Z and Sun, X and Chen, J and Yu, Y and Ni, Z and Wang, Y},
title = {Identification of the full-length GbERD7 gene family in Gossypium barbadense and functional analysis of the role of the GbERD7g gene in drought and salt tolerance.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {360},
number = {},
pages = {112715},
doi = {10.1016/j.plantsci.2025.112715},
pmid = {40840863},
issn = {1873-2259},
mesh = {*Gossypium/genetics/physiology ; Plant Proteins/genetics ; *Salt Tolerance/genetics/physiology ; Droughts ; Dehydration/genetics/metabolism ; *Stress, Physiological/genetics/physiology ; Computational Biology ; Genes, Plant ; *Acclimatization/genetics/physiology ; Sodium Chloride ; Polyethylene Glycols ; Hot Temperature ; Malondialdehyde/metabolism ; },
abstract = {ERD (early response to dehydration) genes are promptly upregulated under dehydration stress and are pivotal in plant development. Nonetheless, the precise impact of the ERD7 gene on the response of cotton to abiotic stress remains unclear. The physical and chemical characteristics, gene architecture, gene collinearity, and transcriptomic profiles were examined. Using bioinformatics techniques, we investigated the evolutionary relationships among the genes within the GbERD7 gene family of sea island cotton. The GbERD7 genes are unevenly distributed across the seven chromosomes of sea island cotton, with multiple gene duplications. The GbERD7 gene family was subjected to phylogenetic analysis, leading to the classification of its members into the SENA and SENB subfamilies. The expression of the GbERD7 genes was investigated in relation to heat, low-temperature, salt (NaCl), and polyethylene glycol (PEG) treatments. Some genes presented greater expression in specific organs and different periods of fiber development. The functional role of GbERD7g was subsequently investigated using molecular biological techniques. GbERD7g exhibited pronounced expression in sea island cotton leaves and was upregulated following exposure to PEG, NaCl, and ABA. Subcellular localization studies revealed that the GbERD7g protein is located within the nucleus as well as the plasma membrane of the cell. When the GbERD7g gene was silenced under drought and salt stress, the sea island cotton plants were significantly less resistant to drought and salinity and exhibited lower survival than the control plants. The proline levels, catalase activity, and superoxide dismutase activity were reduced, and the malondialdehyde and hydrogen peroxide levels were elevated. In addition, compared with those in the control plants, the expression of all three stress-responsive genes, namely, GbRD22, GbRD26, and GbCDPK1, was significantly lower in the mutant plants.},
}

*Gossypium/genetics/physiology
Plant Proteins/genetics
*Salt Tolerance/genetics/physiology
Droughts
Dehydration/genetics/metabolism
*Stress, Physiological/genetics/physiology
Computational Biology
Genes, Plant
*Acclimatization/genetics/physiology
Sodium Chloride
Polyethylene Glycols
Hot Temperature
Malondialdehyde/metabolism

@article {pmid40841201,
year = {2025},
author = {Sena, AVDS and Telles, L and Melo, PHM and Salomão, SL and Uzeda, TS and Pereira Lima, BL and Kratky, L and Mooney, DP and Bustorff-Silva, J},
title = {The management of cryptorchidism in Brazil: An ecological overview.},
journal = {Journal of pediatric urology},
volume = {21},
number = {6},
pages = {1813-1819},
doi = {10.1016/j.jpurol.2025.07.025},
pmid = {40841201},
issn = {1873-4898},
mesh = {Humans ; *Cryptorchidism/surgery/epidemiology ; Male ; Brazil/epidemiology ; *COVID-19/epidemiology ; Child ; Child, Preschool ; *Orchiopexy/statistics & numerical data ; Infant ; Adolescent ; Infant, Newborn ; },
abstract = {INTRODUCTION: Cryptorchidism refers to the extra-scrotal location of the testicle and is the most common male genital anomaly. Although the recommended age ranges for both hormonal and surgical treatments are well-established, within the Brazilian Unified Health System (SUS), children with cryptorchidism undergo surgery at varying ages across the country. As a time-sensitive procedure, delayed orchidopexy has consequences such as an increased risk of infertility or even testicular cancer. Correlating data on cryptorchidism treatment in SUS with geographic and socioeconomic indicators may help to understand how a population's profile influences the public healthcare system. This study explores the potential relationship between the age at which orchiopexy is performed and the quality of public healthcare services in Brazil while also assessing the impact of the COVID-19 pandemic on this surgery's backlog.

METHODS: To achieve this, we collected data from the Department of Informatics of the Brazilian Public Health System (DATASUS) and indicators provided by the Brazilian Institute of Geography (IBGE) and the Institute for Applied Economic Research (IPEA). We cataloged and compiled the data for comprehensive analysis.

RESULTS: Between 2008 and 2022, 94,237 orchiopexies were performed in SUS in patients aged 0-15. Nationwide, this represents only 47.6 % of the expected procedures, ranging from 22.75 % in the North to 68.18 % in the South. The proportion of surgeries performed before age 2 was very low, ranging from 12 % in the North and Northeast to 24 % in the South. Most orchiopexies in Brazil were performed after the age of five. The COVID-19 pandemic significantly worsened this situation, causing a 44.45 % decline in surgeries in 2020 compared to 2019, disproportionately affecting all age groups and exacerbating the backlog of surgeries.

CONCLUSION: Our study indicates that many children with cryptorchidism remain undiagnosed or receive delayed treatment. The COVID-19 pandemic further worsened this scenario, temporarily reducing the number of operations. These findings underscore the urgent need for comprehensive public policies to improve healthcare access and prevent complications associated with untreated cryptorchism.},
}

Humans
*Cryptorchidism/surgery/epidemiology
Male
Brazil/epidemiology
*COVID-19/epidemiology
Child
Child, Preschool
*Orchiopexy/statistics & numerical data
Infant
Adolescent
Infant, Newborn

@article {pmid40841825,
year = {2025},
author = {De Rovere, F and Mastropierro, M and Jungclaus, JH and Khodri, M and Rubino, A and Zanchettin, D},
title = {Future Atlantification of the European Arctic limited under sustained global warming.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30802},
pmid = {40841825},
issn = {2045-2322},
support = {2022CCRN7R, "ATTRACTION - ATlantificaTion dRiven by polAr-subpolar ConnecTIONs", CUP: H53D23001550006//Next-GenerationEU - PNRR - M.4 C.2, INVESTIMENTO 1.1 - PRIN22/ ; },
abstract = {Atlantification is an ongoing oceanic phenomenon characterised by the expansion of the typical Atlantic domain towards the Arctic, driving rapid oceanic and ecological changes in the European Arctic. Using reanalyses and a multi-model ensemble of unperturbed and transient preindustrial, historical and future-scenario simulations, this study shows that modern Atlantification possibly initiated in the late nineteenth century, preceded by several "Arctification" episodes in the preindustrial millennium. In the historical period, Atlantification and pan-Arctic warming superposed constructively to drive upper-ocean warming and salinification in the Barents Sea. Modern Atlantification is projected to continue in the next few decades, fully revealing its exceptional character in the context of the past millennium. However, Atlantification halts during the second half of the twenty-first century, decoupling from pan-Arctic warming. The northward expansion of the Atlantic domain is hindered by the onset of a damping mechanism where the Atlantic-Arctic density gradient increases progressively, which sustains a countercurrent by baroclinic adjustment pushing the Arctic polar front southward. As the evolution of this density gradient is intertwined with the retreat of the sea-ice edge, a late-summer ice-free Barents Sea may mark the end of modern Atlantification.},
}

@article {pmid40843346,
year = {2025},
author = {Xia, K and Hu, Y and Cai, S and Lin, M and Lu, M and Lu, H and Ye, Y and Lin, F and Gao, L and Xia, Q and Tian, R and Lin, W and Xie, L and Tan, D and Lu, Y and Lin, X and Yang, X and Zhong, L and Xu, L and Zhang, Z and Wang, L and Ren, J and Xu, H},
title = {GastritisMIL: An interpretable deep learning model for the comprehensive histological assessment of chronic gastritis.},
journal = {Patterns (New York, N.Y.)},
volume = {6},
number = {8},
pages = {101286},
pmid = {40843346},
issn = {2666-3899},
abstract = {The comprehensive histological assessment of chronic gastritis is imperative for guiding endoscopic follow-up strategies and surveillance of early-stage gastric cancer, yet rapid and objective assessment remains challenging in clinical workflows. We propose a powerful deep learning model (GastritisMIL) to effectively identify pathological alterations on H&E-stained biopsy slides, thereby expediting pathologists' evaluation and improving decision-making regarding follow-up intervals. We have trained and tested GastritisMIL by using retrospective data from 2,744 patients and evaluated discriminative performance across three medical centers (467 patients). GastritisMIL attained areas under the receiver operating curve greater than 0.971 in four tasks (inflammation, activity, atrophy, and intestinal metaplasia) and superior performance comparable to that of two senior pathologists. Specifically, interpretable attention heatmaps generated by GastritisMIL effectively assist junior pathologists in locating suspicious lesion regions across the entire field and minimizing missed diagnosis risk. Moreover, the high generalizability of this developed model across multiple external cohorts demonstrates its potential translational value.},
}

@article {pmid40846910,
year = {2025},
author = {Lu, M and Wang, S and Zhou, Y and Wang, X and Su, H and Gong, Y and De, J},
title = {Multi-omics profiling reveals single-seed mutants of Ephedra saxatilis as dominant variants in high-altitude Xizang.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1118},
pmid = {40846910},
issn = {1471-2229},
support = {32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; 32060087//National Natural Science Foundation of China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202402ZD0005//Science and Technology Projects of Xizang Autonomous Region, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; XZ202501ZY0101//Xizang Autonomous Region Science and Technology Department project, China/ ; },
mesh = {*Altitude ; *Ephedra/genetics/metabolism/physiology ; Germination/genetics ; *Seeds/genetics/metabolism/ultrastructure/physiology ; Tibet ; Mutation ; Metabolomics ; Transcriptome ; Multiomics ; },
abstract = {Ephedra species, important Tibetan medicinal plants, are widely distributed across the Qinghai-Tibet Plateau at altitudes of 2700-5000 m. Their adaptation to high-altitude environments, such as low temperatures, strong UV radiation and low oxygen, is still poorly understood. This study investigated the morphological, metabolic, and genetic mechanisms underlying the reproductive advantage of a unique single-seed variant observed in high-germination-rate Ephedra species. Seeds from six Ephedra species were collected for germination assays and electron microscopic analysis. Results showed that E. saxatilis, E. intermedia, and E. monosperma exhibited significantly higher germination rates (Germination rates > 65%) and predominantly produced single-seed variants, while others mainly produced double seeds. Analysis of burr and fold numbers of phenotypic traits showed a significant positive correlation with germination rates. Time-course metabolomics analysis identified 762 KEGG annotated metabolites, and revealed E. saxatilis as the dominant species due to its faster metabolic rate, particularly simulated high-altitude conditions. Absolute hormone quantification highlighted the single-seed variant of E. saxatilis as the dominant type, with ABA content peaking in the shed seed coat. ABA exhibited antagonistic interactions with 2MeScZR, SA, IAA, GA7, IPR, and t-CA, suggesting a complex hormonal regulation network. Co-expression network analysis integrating transcriptome and hormone data predicted 23 key genes regulating seed germination adaptation. This study provides novel insights into the ecological and evolutionary significance of single-seed variation in high-altitude adaptation. The findings have potential applications in high-altitude plant breeding, conservation, and sustainable utilization of Ephedra species. Future research should focus on the genetic basis of single-seed variation and its role in other high-altitude plant species.},
}

*Altitude
*Ephedra/genetics/metabolism/physiology
Germination/genetics
*Seeds/genetics/metabolism/ultrastructure/physiology
Tibet
Mutation
Metabolomics
Transcriptome
Multiomics

@article {pmid40848298,
year = {2025},
author = {Jia, Y and Chen, L and Jin, LN and Zhang, P and Chen, L and Fan, C and Liu, H and Ji, Y and Li, D and Chen, J},
title = {Environmentally Relevant Levels of Ozone Enhance Klebsiella pneumoniae Pulmonary Colonization and Cross-Organ Translocation.},
journal = {Environmental science & technology},
volume = {59},
number = {35},
pages = {18424-18439},
doi = {10.1021/acs.est.5c02782},
pmid = {40848298},
issn = {1520-5851},
mesh = {*Klebsiella pneumoniae ; *Ozone/toxicity ; Animals ; Lung/microbiology ; Mice ; Klebsiella Infections ; },
abstract = {Ozone (O3) is a major global air pollutant. Recent epidemiological studies have suggested links between O3 exposure and outbreaks of infectious diseases. However, whether environmentally relevant levels of O3 exacerbate the colonization and infection of airborne pathogens remains unclear. This study demonstrated that exposure to environmentally relevant levels of O3 (0.15 and 0.60 ppm) significantly enhanced pulmonary colonization of low-dose Klebsiella pneumoniae (1 × 10[3] CFU/mouse) in mice, which failed to colonize without O3 exposure. Unexpectedly, in vivo and in vitro coculture experiments with BEAS-2B bronchial epithelial cells demonstrated that O3 exposure also enhanced the ability of K. pneumoniae to penetrate the lung-blood barrier, thereby inducing bacteremia that spread to the liver and caused severe liver injury. O3 exposure reduced the proportions of T cells, B cells, and macrophages in the lungs and altered the expression of key pulmonary genes (Tlr4, Il-18, Traf6, and Tgf-β1) involved in resisting K. pneumoniae colonization. In addition, lipid peroxidation product MDA in plasma acted as a mediator in the signal transmission along the lung-liver axis. This study underscores the critical role of air pollutants in pathogen colonization and infection, emphasizing the urgent need to address air quality to mitigate respiratory health risks.},
}

*Klebsiella pneumoniae
*Ozone/toxicity
Animals
Lung/microbiology
Mice
Klebsiella Infections

@article {pmid40851520,
year = {2025},
author = {Naseri, C and Hill, AM and Xu, D and Francis-Coad, J and Vaz, S and Garswood, L and Meakes, R and Umbella, J and O'Brien, G and Starling, T and Weselman, T},
title = {What influences older people to join a community hub to engage in healthy ageing programs? An exploratory study.},
journal = {Australasian journal on ageing},
volume = {44},
number = {3},
pages = {e70079},
pmid = {40851520},
issn = {1741-6612},
support = {//Royal Perth Hospital Medical Research Foundation/ ; //Australian Association of Gerontology Research Trust/ ; },
mesh = {Humans ; *Healthy Aging/psychology ; Aged ; Female ; Male ; Western Australia ; Aged, 80 and over ; Age Factors ; Middle Aged ; *Health Services for the Aged/organization & administration ; Social Support ; Social Networking ; Interviews as Topic ; *Community Health Services ; *Health Promotion ; Qualitative Research ; *Community Networks/organization & administration ; },
abstract = {OBJECTIVES: Most people seek to stay connected to their community as they age; this has been a major focus in the development of innovative community programs in Australia. This study aimed to explore what influences older people to join a community hub to engage in healthy ageing programs.

METHODS: Semi-structured interviews (n = 29) were conducted during an Open Day in early 2023 at an urban community hub in Western Australia, followed by telephone interviews (n = 9) of a purposive sample of older individuals, community hub facilitators and coordinators of national community hubs. Analysis used a socio-ecological framework.

RESULTS: Deductive content analysis identified social prescribing as an overarching influencer for older people to join and engage in healthy ageing programs and main themes of (i) supporting community hub facilitators to harness community assets, (ii) link-supports provided to older members by paid community hub concierges triggered positive outcomes at individual and community levels, (iii) online and in-person social and physical healthy ageing activities tailored to member interests and (iv) nurturing social networks and reciprocity between members sustained engagement in healthy ageing activities.

CONCLUSIONS: The dynamic process of social prescribing was a central influencer for older adults to engage in healthy ageing programs, and the social network perpetuated through community hubs was an immeasurable social investment that boosted the resilience of intergenerational populations in Australian communities. Policy support is required for communities to meet the challenge of being responsive to the needs of members who seek to remain independent as they age in place.},
}

Humans
*Healthy Aging/psychology
Aged
Female
Male
Western Australia
Aged, 80 and over
Age Factors
Middle Aged
*Health Services for the Aged/organization & administration
Social Support
Social Networking
Interviews as Topic
*Community Health Services
*Health Promotion
Qualitative Research
*Community Networks/organization & administration

@article {pmid40854001,
year = {2025},
author = {Khajehnejad, M and García, J and Meyer, B},
title = {Age polyethism can emerge from social learning: A game-theoretic investigation.},
journal = {PLoS computational biology},
volume = {21},
number = {8},
pages = {e1013415},
pmid = {40854001},
issn = {1553-7358},
mesh = {Animals ; *Social Learning/physiology ; *Game Theory ; Behavior, Animal/physiology ; Social Behavior ; Computational Biology ; Models, Biological ; },
abstract = {Age-polyethism-the age-based allocation of tasks in social insect colonies-is a key feature of division of labour. While its hormonal underpinnings have been studied extensively, the behavioural and environmental mechanisms driving age-polyethism remain poorly understood, especially under ecological stress. We present a novel modelling framework that integrates social learning with task-related environmental feedback to explain the emergence and breakdown of age-polyethism. We develop two models: a Social Learning (SL) model, in which individuals adapt task preferences by copying similar peers, and a Stimulus-Response Threshold Social Learning (SRT-SL) model, which extends this framework by incorporating task-related dynamic stimuli and response thresholds that regulate collective task demand. Our models demonstrate that age-polyethism can emerge from simple social imitation processes, without the need for fixed hormonal schedules. We show that under increasing environmental pressure (e.g., resource scarcity), age-polyethism collapses as younger individuals are forced into tasks typically handled by older workers. Importantly, we find that age-polyethism does not necessarily optimize immediate colony efficiency; instead, it appears to reflect a trade-off between environmental constraints and behavioural coordination. These findings provide a mechanistic and ecologically grounded explanation for empirical observations linking environmental stress to dysfunctional division of labour and colony collapse.},
}

Animals
*Social Learning/physiology
*Game Theory
Behavior, Animal/physiology
Social Behavior
Computational Biology
Models, Biological

@article {pmid40855644,
year = {2025},
author = {Panneerselvam, K and Tiwari, KK and Licata, L and Panni, S and Ricard-Blum, S and Balu, S and Huget, S and Medina Reyes, JJ and Ragueneau, E and Perfetto, L and Meldal, B and Orchard, S and Hermjakob, H},
title = {Mining Alzheimer's Interactomes, Macromolecular Complexes and Pathways for Drug Discovery.},
journal = {Proteomics},
volume = {25},
number = {21-22},
pages = {102-150},
pmid = {40855644},
issn = {1615-9861},
support = {203149/WT_/Wellcome Trust/United Kingdom ; 218294/WT_/Wellcome Trust/United Kingdom ; U24 HG012198/AOU_/AOU NIH HHS/United States ; U24 HG012198/HG/NHGRI NIH HHS/United States ; 3367/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; //BBSRC - National Science Foundation/Directorate for Biological Sciences/ ; 212925/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; //European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) core funding/ ; },
mesh = {*Alzheimer Disease/metabolism/genetics/drug therapy ; Humans ; *Drug Discovery/methods ; Amyloid beta-Protein Precursor/metabolism/genetics ; Protein Interaction Maps ; MicroRNAs/metabolism/genetics ; Data Mining ; Mutation ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder that leads to dementia. Many cases are diagnosed annually and there is no currently available cure. Understanding the underlying disease biology of AD through the study of molecular networks, particularly by mapping clinical variants to tissue-specific interactomes and regulatory macromolecular assemblies, offers a promising avenue to elucidate altered disease pathways. In this study, we applied differential interactome analysis using a manually curated AD dataset to identify how disease-associated mutations alter both transient and stable protein interactions. By focussing on variant-specific associations detected in brain-relevant tissues, we mapped disruptions in stable macromolecular assemblies and performed Reactome enrichment analysis to uncover perturbed pathways unique to each variant. Additionally, we explored therapeutic insights through the analysis of amyloid precursor protein (APP) physical interactors, identifying potential intervention points that influence amyloidogenic processing. Complementing protein-level data, we integrated microRNA (miRNA)-mediated regulatory interactions, revealing an additional layer of posttranscriptional control over key AD genes. Together, this multilayered strategy provides a framework for precision therapeutics in AD.},
}

*Alzheimer Disease/metabolism/genetics/drug therapy
Humans
*Drug Discovery/methods
Amyloid beta-Protein Precursor/metabolism/genetics
Protein Interaction Maps
MicroRNAs/metabolism/genetics
Data Mining
Mutation

@article {pmid40858627,
year = {2025},
author = {Ge, S and Li, J and Ma, H and Sánchez-Bermúdez, M and Wu, S and Lv, Q and Guo, F and Dong, J and Ma, G and Li, QQ and Satheesh, V and Lei, M},
title = {A cis-natural antisense RNA regulates alternative polyadenylation of SlSPX5 under Pi starvation in tomato.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7981},
pmid = {40858627},
issn = {2041-1723},
support = {U24A20385//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270344//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025JCXK01//Hangzhou Normal University (HNU)/ ; 2347540//National Science Foundation (NSF)/ ; },
mesh = {*Polyadenylation/genetics ; *Solanum lycopersicum/genetics/metabolism ; Gene Expression Regulation, Plant ; *RNA, Antisense/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Phosphates/deficiency/metabolism ; RNA, Messenger/metabolism/genetics ; Transcription Factors/metabolism/genetics ; RNA Polymerase II/metabolism ; },
abstract = {Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3' ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene SlSPX5, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a cis-natural antisense RNA (cis-NAT) is activated from SlSPX5 to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this cis-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5' end of SlSPX5. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.},
}

*Polyadenylation/genetics
*Solanum lycopersicum/genetics/metabolism
Gene Expression Regulation, Plant
*RNA, Antisense/genetics/metabolism
*Plant Proteins/genetics/metabolism
*Phosphates/deficiency/metabolism
RNA, Messenger/metabolism/genetics
Transcription Factors/metabolism/genetics
RNA Polymerase II/metabolism

@article {pmid40862956,
year = {2025},
author = {Yoon, HJ and Seo, JH and Shin, SH and Abdelhamid, MAA and Pack, SP},
title = {Bioinformation and Monitoring Technology for Environmental DNA Analysis: A Review.},
journal = {Biosensors},
volume = {15},
number = {8},
pages = {},
pmid = {40862956},
issn = {2079-6374},
support = {RS-2021NR060107//the National Research Foundation of Korea funded by the Ministry of Science and ICT/ ; RS-2022-NR074662//the National Research Foundation of Korea funded by the Ministry of Education/ ; },
mesh = {*Environmental Monitoring/methods ; *DNA, Environmental/analysis ; *Computational Biology ; Ecosystem ; },
abstract = {Environmental DNA (eDNA) analysis has emerged as a transformative tool in environmental monitoring, enabling non-invasive detection of species and microbial communities across diverse ecosystems. This study systematically reviews the role of bioinformation technology in eDNA analysis, focusing on methodologies and applications across air, soil, groundwater, sediment, and aquatic environments. Advances in molecular biology, high-throughput sequencing, bioinformatics tools, and field-deployable detection systems have significantly improved eDNA detection sensitivity, allowing for early identification of invasive species, monitoring ecosystem health, and tracking pollutant degradation processes. Airborne eDNA monitoring has demonstrated potential for assessing microbial shifts due to air pollution and tracking pathogen transmission. In terrestrial environments, eDNA facilitates soil and groundwater pollution assessments and enhances understanding of biodegradation processes. In aquatic ecosystems, eDNA serves as a powerful tool for biodiversity assessment, invasive species monitoring, and wastewater-based epidemiology. Despite its growing applicability, challenges remain, including DNA degradation, contamination risks, and standardization of sampling protocols. Future research should focus on integrating eDNA data with remote sensing, machine learning, and ecological modeling to enhance predictive environmental monitoring frameworks. As technological advancements continue, eDNA-based approaches are poised to revolutionize environmental assessment, conservation strategies, and public health surveillance.},
}

*Environmental Monitoring/methods
*DNA, Environmental/analysis
*Computational Biology
Ecosystem

@article {pmid40872272,
year = {2025},
author = {Bugingo, C and Infantino, A and Okello, P and Perez-Hernandez, O and Petrović, K and Turatsinze, AN and Moparthi, S},
title = {From Morphology to Multi-Omics: A New Age of Fusarium Research.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40872272},
issn = {2076-0817},
mesh = {*Fusarium/genetics/classification/pathogenicity ; Genomics/methods ; *Plant Diseases/microbiology ; Mycotoxins ; Humans ; Crops, Agricultural/microbiology ; Host-Pathogen Interactions ; *Fusariosis/microbiology ; Multiomics ; },
abstract = {The Fusarium genus includes some of the most economically and ecologically impactful fungal pathogens affecting global agriculture and human health. Over the past 15 years, rapid advances in molecular biology, genomics, and diagnostic technologies have reshaped our understanding of Fusarium taxonomy, host-pathogen dynamics, mycotoxin biosynthesis, and disease management. This review synthesizes key developments in these areas, focusing on agriculturally important Fusarium species complexes such as the Fusarium oxysporum species complex (FOSC), Fusarium graminearum species complex (FGSC), and a discussion on emerging lineages such as Neocosmospora. We explore recent shifts in species delimitation, functional genomics, and the molecular architecture of pathogenicity. In addition, we examine the global burden of Fusarium-induced mycotoxins by examining their prevalence in three of the world's most widely consumed staple crops: maize, wheat, and rice. Last, we also evaluate contemporary management strategies, including molecular diagnostics, host resistance, and integrated disease control, positioning this review as a roadmap for future research and practical solutions in Fusarium-related disease and mycotoxin management. By weaving together morphological insights and cutting-edge multi-omics tools, this review captures the transition into a new era of Fusarium research where integrated, high-resolution approaches are transforming diagnosis, classification, and management.},
}

*Fusarium/genetics/classification/pathogenicity
Genomics/methods
*Plant Diseases/microbiology
Mycotoxins
Humans
Crops, Agricultural/microbiology
Host-Pathogen Interactions
*Fusariosis/microbiology
Multiomics

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

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

@article {pmid40885803,
year = {2025},
author = {Simonienko, K and Jermakowicz, E and Szefer, P and Wróbel, K and Suprunowicz, U and Cwalina, U and Kostro-Ambroziak, A},
title = {The impact of urban flower meadows on the well-being of city dwellers provides hints for planning biophilic green spaces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31981},
pmid = {40885803},
issn = {2045-2322},
support = {SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; SKN/SP/495977/2021//Ministry of Science and Higher Education/ ; },
mesh = {Humans ; Female ; Male ; *Flowers/growth & development ; Adult ; Middle Aged ; Cities ; *Urban Population ; Emotions ; Young Adult ; Aged ; },
abstract = {Living surrounded by greenery has a relaxing effect and reduces physiological and psychological symptoms of stress. In view of the exponential growth of the urban population and disconnection with nature, supporting the physical and mental health of city dwellers is a huge challenge nowadays. In this context, urban flower meadows (UFMs), a relatively new management strategy cultivated in many cities, can be a very important component of urban greenery, which support human well-being. We investigated the emotional reception of UFMs, taking into account the features of different types of UFMs and the socio-demographic characteristics of respondents. Our research shows that urban flower meadows evoke positive emotions regardless of the age, gender and place of origin of respondents. While some structural variables of UFMs, particularly the proportion of green in relation to other colours, the representation of various flower colours, the proportion of yellow flowers, and the presence of alien plant species-influence people's perception. Fewer colours and the absence of alien plant species tend to shift perception towards less positive emotions. The dominance of yellow flowers evokes positive emotions. These results are helpful for the further planning of UFMs to better reinforce the well-being of all city dwellers.},
}

Humans
Female
Male
*Flowers/growth & development
Adult
Middle Aged
Cities
*Urban Population
Emotions
Young Adult
Aged

@article {pmid40886889,
year = {2025},
author = {Furxhi, I and Perucca, M and Baldi, G and Dami, V and Cioni, A and Koivisto, AJ and Bengalli, R and Mantecca, P and Motta, G and Carriere, M and Kose, O and Nicosia, A and Ravegnani, F and Burrueco-Subirà, D and Candalija, A and Cabellos, J and Vázquez-Campos, S and Lahive, E and Eagles, E and de Ipiña, JL and Oliveira, J and Conin, P and Zanoni, I and Brigliadori, A and Faccani, L and Syed, T and Haq, EU and O'Mahony, C and Serantoni, M and Blosi, M and Exner, T and Costa, A},
title = {The fruits of data shepherding: A collection of open FAIR datasets for titanium dioxide coated photocatalytic surfaces.},
journal = {NanoImpact},
volume = {39},
number = {},
pages = {100583},
doi = {10.1016/j.impact.2025.100583},
pmid = {40886889},
issn = {2452-0748},
mesh = {*Titanium/chemistry ; Catalysis ; *Databases, Factual ; Surface Properties ; *Nanostructures/chemistry ; Information Dissemination ; },
abstract = {This paper presents a large-scale collaborative effort within a multi-partner consortium, to systematically structure, curate, and openly share data in alignment with the FAIR principles. The data result from a case study of titanium dioxide (TiO2) nanomaterials (NMs) for photocatalytic depolluting surfaces, produced via various spray coating techniques under the Safe and Sustainable by Design (SSbD) approach. The data are publicly available through a dedicated Zenodo community (https://zenodo.org/communities/asina/records), comprising of individual records that separately host the data and the corresponding metadata. Each dataset is systematically named to reflect its context beginning with "ASINA dataset," followed by i) the relevant life cycle stage (LCS) from synthesis to end-of-life, ii) the SSbD dimension (i.e., functionality, safety, and environmental aspects), and iii) the assessed features (e.g., physicochemical properties, hazard evaluation, functionality assessment) facilitating searchability. The data files include "descriptors" excel tab, which is a harmonized version derived from primary data for visualization, data integration and future modeling applications. Metadata are provided in separate records and include detailed information such as contributor name and affiliations, experimental protocols, instrumentation, dictionary definitions, ontologies, and licensing terms. The data and metadata files are mutually paired in Zenodo using related identifiers, where each data file includes the DOI of its corresponding metadata file, and vice versa. In total, 43 interlinked records are provided capturing the case study, offering structured and machine-actionable resources that support modeling, data integration and harmonization efforts within the nanosafety and nanoinformatics communities. This effort was coordinated through dedicated data shepherding, which enabled trust-building, metadata alignment, and consistent FAIR implementation across partners.},
}

*Titanium/chemistry
Catalysis
*Databases, Factual
Surface Properties
*Nanostructures/chemistry
Information Dissemination

@article {pmid40887834,
year = {2025},
author = {Han, Y and Yu, J and Liu, X and Zhang, F and Huang, X and Lu, Y and Zhang, W and Zimmerman, R and Rudich, Y and Li, Q and Chen, J and Chen, Y and Jin, LN},
title = {Generation of More Potent Components at Higher Temperatures Offsets Toxicity Reduction despite Reduced Mass Emissions during Biomass Burning.},
journal = {Environmental science & technology},
volume = {59},
number = {36},
pages = {19244-19256},
doi = {10.1021/acs.est.5c05710},
pmid = {40887834},
issn = {1520-5851},
mesh = {*Biomass ; Humans ; Temperature ; Aerosols ; Air Pollutants/toxicity ; Reactive Oxygen Species ; },
abstract = {Biomass burning organic aerosols (BBOAs) represent a major global health hazard. Their toxicity varies significantly due to the diversity of combustion conditions, which shape mixtures of components with differing toxic potency. We quantified component-specific contributions to intracellular reactive oxygen species generation in human bronchial epithelial cells exposed to BBOAs produced under controlled combustion conditions. Elevated combustion temperatures substantially reduced organic carbon (OC) mass emissions (by 20-fold) but resulted in a more modest reduction in OC toxicity emissions (by 5-fold). The toxicity emission reduction was primarily attributed to water-extractable OC (WOC), while methanol-extractable OC (MOC) limited this effect. The reduced emission of WOC toxicity was driven by the decreased mass emission of polar compounds such as methoxylates, as the toxicity per unit mass of WOC showed negligible changes across temperatures. In contrast, the toxicity per unit mass of MOC increased 10-fold from low to high temperatures, partially due to the formation of more potent aromatic derivatives, despite their smaller mass contribution. These findings underscore the importance of identifying key toxicity drivers to guide targeted source apportionment and refine strategies for reducing toxic emissions.},
}

*Biomass
Humans
Temperature
Aerosols
Air Pollutants/toxicity
Reactive Oxygen Species

@article {pmid40888850,
year = {2026},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1733-D1742},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Skłodowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}

*Plant Roots/microbiology
*Microbiota/genetics
*Databases, Protein
Metagenomics
Molecular Sequence Annotation
Metagenome

@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsrådet Formas/ ; },
mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}

*Metagenomics/methods
*Dental Calculus/microbiology
*Mammals/microbiology/classification
Animals
*Microbiota
*Gene Library
Metagenome
Computational Biology

@article {pmid40892020,
year = {2025},
author = {Ng, S and Brown, JP and Straub, L and Bateman, B and Gray, KJ and Huybrechts, KF and Hernández-Díaz, S},
title = {Leveraging Health Insurance Claims Data to Complement the Centers for Disease Control and Prevention Surveillance System for Birth Defects.},
journal = {Birth defects research},
volume = {117},
number = {9},
pages = {e2523},
pmid = {40892020},
issn = {2472-1727},
support = {R01 HD097778/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; United States/epidemiology ; *Congenital Abnormalities/epidemiology ; Female ; Prevalence ; Centers for Disease Control and Prevention, U.S. ; Infant, Newborn ; *Insurance, Health/statistics & numerical data ; Pregnancy ; Databases, Factual ; Male ; Insurance Claim Review ; Population Surveillance/methods ; Infant ; Adult ; },
abstract = {BACKGROUND: Birth defect surveillance can help identify temporo-spatial clusters and teratogenic signals to inform subsequent investigations or interventions. In the United States, state surveillance systems exist but collect limited information, prompting a complementary use of health insurance claims data to describe national birth defect prevalence trends and investigate signals.

METHODS: The Merative MarketScan Commercial Claims and Encounters (MarketScan) database was used to identify liveborn infants from 2016 to 2022, with linkage to maternal health care records during pregnancy. Birth defects were identified using ICD-10-CM codes recorded in the first 3 months of life, and prevalence estimates with 95% confidence intervals were generated for birth defect categories and select birth defects.

RESULTS: The study population included 943,855 liveborn infants. From 2016 to 2022, the prevalence increased for cardiac, central nervous system, ear, genital, urinary, musculoskeletal, and limb birth defect categories. Stable prevalence over the study period was observed for chromosomal, oral cleft, respiratory, gastrointestinal, vascular, and eye defects. For specific defects, we observed an increased prevalence of both ankyloglossia and lip-tie over the study period and a transient higher prevalence of omphalocele over 2017 and 2018. Within genital birth defects, we observed increasing prevalence trends for congenital malformations of the penis, while hypospadias and cryptorchidism remained relatively stable.

CONCLUSION: Health care utilization databases can complement existing surveillance systems by generating, confirming, or refuting signals based on ecological trends or clusters. The availability of patient information in claims databases can allow for further investigation of signals to inform birth defect etiology.},
}

Humans
United States/epidemiology
*Congenital Abnormalities/epidemiology
Female
Prevalence
Centers for Disease Control and Prevention, U.S.
Infant, Newborn
*Insurance, Health/statistics & numerical data
Pregnancy
Databases, Factual
Male
Insurance Claim Review
Population Surveillance/methods
Infant
Adult

@article {pmid40892908,
year = {2025},
author = {Araujo, G and Lurgi, M},
title = {Mutualism provides a basis for biodiversity in eco-evolutionary community assembly.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013402},
pmid = {40892908},
issn = {1553-7358},
mesh = {*Biodiversity ; *Symbiosis/physiology ; *Biological Evolution ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; Computer Simulation ; },
abstract = {Unveiling the ecological and evolutionary mechanisms underpinning the assembly of stable and complex ecosystems is a main focus of community ecology. Ecological theory predicts the necessity of structural constraints on the network of species interactions to allow for growth and persistence of multi-species communities. However, the mechanisms behind their emergence are not well understood. An understanding of how the coexistence of diverse species interaction types could influence the development of complexity and how a persistent composition of interactions could arise in nature is needed. Using an eco-evolutionary model, we investigate the assembly of complex species interaction networks with multiple interaction types and its consequences for ecosystem stability. Our results show that highly mutualistic communities promote complex and stable network configurations, thus resulting in a positive complexity-stability relationship. We show that evolution by speciation enhances the emergence of such conditions compared to a purely ecological assembly scenario of repeated invasions by migrating species. Furthermore, communities evolved in isolation promote a disproportionately higher complexity and a larger diversity of outcomes. Our results produce valuable theoretical insight into the mechanisms behind the emergence of ecological complexity and into the roles of mutualism and speciation in community formation.},
}

*Biodiversity
*Symbiosis/physiology
*Biological Evolution
*Models, Biological
*Ecosystem
Computational Biology
Animals
Computer Simulation

@article {pmid40892914,
year = {2025},
author = {Rowntree, LC and Allen, LF and Hagen, RR and McQuilten, HA and Quadeer, AA and Chaurasia, P and Kaewpreedee, P and Lee, KWK and Cohen, CA and Petersen, J and Littler, DR and Habel, JR and Zhang, W and Cheng, SMS and Chan, KKP and Kwok, JSY and Leung, KSM and Wu, JT and Lee, CK and Davies, J and Pannaraj, PS and Kaity Allen, E and Thomas, PG and Tosif, S and Crawford, NW and Lappas, M and Thevarajan, I and Lewin, SR and Kent, SJ and Juno, JA and Bond, KA and Williamson, DA and Holmes, NE and Smibert, OC and Gordon, CL and Trubiano, JA and Kotsimbos, TC and Cheng, AC and Efstathiou, C and Turtle, L and Thwaites, RS and Brightling, CE and , and Rossjohn, J and McKay, MR and Tian, J and Liu, WJ and Gao, GF and Xu, J and Sonehara, K and Ishii, KJ and Namkoong, H and Okada, Y and Peiris, M and Hui, DSC and Poon, LLM and Doherty, PC and Nguyen, THO and Valkenburg, SA and Kedzierska, K},
title = {HLA-B*15:01-positive severe COVID-19 patients lack CD8[+] T cell pools with highly expanded public clonotypes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {36},
pages = {e2503145122},
pmid = {40892914},
issn = {1091-6490},
support = {U01 AI144616/AI/NIAID NIH HHS/United States ; 1173871//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Humans ; *COVID-19/immunology/genetics ; *CD8-Positive T-Lymphocytes/immunology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Spike Glycoprotein, Coronavirus/immunology ; },
abstract = {Understanding host factors driving asymptomatic versus severe disease outcomes is of key importance if we are to control emerging and re-emerging viral infections. HLA-B*15:01 has been associated with asymptomatic SARS-CoV-2 infection in nonhospitalized individuals of European ancestry, with protective immunity attributed to preexisting cross-reactive CD8[+] T-cells directed against HLA-B*15:01-restricted Spike-derived S919-927 peptide (B15/S919[+]CD8[+] T-cells). However, fundamental questions remained on the abundance and clonotypic nature of CD8[+] T-cell responses in HLA-B*15:01-positive patients who succumbed to life-threatening COVID-19. Here, we analyzed B15/S919[+]CD8[+] T-cell responses in COVID-19 patients from independent HLA-typed COVID-19 patient cohorts across three continents, Australia, Asia and Europe. We assessed B15/S919[+]CD8[+] T-cells in COVID-19 patients across disease outcomes ranging from asymptomatic to hospitalized critical illness. We found that severe/critical COVID-19 patients mounted B15/S919[+]CD8[+] T-cell responses lacking a highly expanded key public B15/S919[+]CD8[+] T-cell receptor (TCR; TRAV9-2/TRBV7-2) which recurred across multiple individuals in COVID-19 patients with a mild disease. Instead, B15/S919[+]CD8[+] T-cell responses in life-threatening disease had a prevalence of an alternate TCR clonotypic motif (TRAV38-2/DV8/TRBV20-1), potentially contributing, at least in part, to why B15/S919[+]CD8[+] T-cells in severe COVID-19 patients were less protective. Interestingly, the frequency, memory phenotype, and activation profiles of circulating B15/S919[+]CD8[+] T-cells did not differ across disease severity. Moreover, B15/S919[+]CD8[+] T-cells were better maintained into convalescence compared to other SARS-CoV-2-specificities. Our study thus provides evidence on the differential nature of the TCR clonal repertoire in 22.37% of HLA-B*15:01-positive COVID-19 patients who developed severe or critical disease in our cohorts, comparing to HLA-B*15:01-expressing individuals with mild COVID-19.},
}

Humans
*COVID-19/immunology/genetics
*CD8-Positive T-Lymphocytes/immunology
*SARS-CoV-2/immunology
Male
Female
Middle Aged
Adult
Aged
Spike Glycoprotein, Coronavirus/immunology

@article {pmid40894108,
year = {2025},
author = {de Goeij, JM and Mueller, B and Achlatis, M and Campana, S and Hudspith, M and Kornder, NA and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet & Donadey, 1987, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {344},
pmid = {40894108},
issn = {2398-502X},
abstract = {We present a scaffold-level genome assembly from a Halisarca caerulea specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium AqS2 ((Tethybacterales) were identified.},
}

@article {pmid40894110,
year = {2025},
author = {Whiteford, S and , and , and , and , and , },
title = {The genome sequence of the virgin bagworm, Luffia ferchaultella (Stephens, 1850).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {108},
pmid = {40894110},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Luffia ferchaultella (the Virgin Bagworm; Arthropoda; Insecta; Lepidoptera; Psychidae). The genome sequence spans 645.30 megabases. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,416 protein-coding genes.},
}

@article {pmid40897756,
year = {2025},
author = {Zhang, F and Liang, Y and Hu, Z},
title = {Research on the inversion model of soil moisture content based on a novel ReMPDI index in mining areas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32330},
pmid = {40897756},
issn = {2045-2322},
support = {N25XQD015//Basic Research Operations in Higher Education/ ; },
abstract = {The excavation of subterranean coal has led to a plethora of ecological and environmental issues, which seriously restrict the sustainable development of society. As one of the important physical indicators of soil, soil moisture content needs to be scientific, real-time, and comprehensively monitored. Due to the low efficiency of manual measurement, methods based on remote sensing data inversion have received widespread attention and in-depth research in recent years. In this study, a new ReMPDI index (Red edge Modified Perpendicular Drought Index) is constructed, and six retrieval models of soil moisture content based on machine learning algorithms are compared and analyzed, and the accuracy is verified by measured sampling data. The following conclusions were obtained: (1) Using the red edge band as the horizontal axis, and the near infrared band NIR as the vertical axis is the optimal spatial band combination of spectral characteristics for constructing soil lines; (2) The determination coefficient (R2) of ReMPDI index based on REdge-NIR spectral feature space and adding vegetation cover factor is the highest, which is-0. 798, and there is a significant correlation, which is better than MPDI and PDI index; (3) The model inversion accuracy of the RF is significantly higher than SVM, BPNN, PLSR, CNN, and RBFNN, with an error of only 9.52% compared to the measured results. The results of this study can provide a theoretical basis and technical support for the fine monitoring of surface soil moisture content on a large scale in mining areas.},
}

@article {pmid40897761,
year = {2025},
author = {Rodal, M and Luyssaert, S and Balzarolo, M and Campioli, M},
title = {A global database of net primary production of terrestrial ecosystems.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1534},
pmid = {40897761},
issn = {2052-4463},
mesh = {*Ecosystem ; *Databases, Factual ; *Biomass ; Soil ; Forests ; Grassland ; },
abstract = {Net primary production (NPP) is a fundamental measure of biomass production in ecosystems. In terrestrial biomes, NPP lacks standard measuring protocols and is difficult to measure. Thus, despite decades of research efforts, NPP data are limited and heterogenous. Moreover, there continues to be a lack of global NPP databases containing harmonized estimates for all major ecosystem types and which account for both above- and belowground production. We present a global database containing records for both above- and belowground production for forests, grasslands, arid shrublands, northern peatlands and tundra at 456 sites. The records are reported as annual production (g m[-2]yr[-1]). The NPP data are complemented with detailed site and methodological information, including a method specific estimate for the measurement uncertainty, as well as ancillary data on climatic conditions, soil fertility and management status. This database provides a basis for comparative studies on local, regional and global scales, and may serve as an important benchmarking dataset for the development of DGVMs.},
}

*Ecosystem
*Databases, Factual
*Biomass
Soil
Forests
Grassland

@article {pmid40899150,
year = {2025},
author = {Ürel, H and Benassou, S and Marti, H and Reska, T and Sauerborn, E and Pinheiro Alves De Souza, Y and Perlas, A and Rayo, E and Biggel, M and Kesselheim, S and Borel, N and Martin, EJ and Venegas, CB and Schloter, M and Schröder, K and Mittelstrass, J and Prospero, S and Ferguson, JM and Urban, L},
title = {Nanopore- and AI-empowered microbial viability inference.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40899150},
issn = {2047-217X},
support = {//Helmholtz Principal Investigator Grant/ ; HIDSS-006//Munich School for Data Science/ ; BB/M010996/1//BBSRC/ ; //STFC Food Network+ Scoping Grant/ ; //Helmholtz Association Initiative and Networking Fund/ ; 1336/2004//Vontobel-Stiftung/ ; //University of Zurich/ ; },
mesh = {*Microbial Viability ; *Nanopores ; *Artificial Intelligence ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Escherichia coli/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. Established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity.

RESULTS: We here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable artificial intelligence (AI) tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false-negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our model's generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions.

CONCLUSIONS: While the potential of our computational framework's generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings.},
}

*Microbial Viability
*Nanopores
*Artificial Intelligence
*Nanopore Sequencing/methods
Metagenomics/methods
Escherichia coli/genetics
Computational Biology/methods

@article {pmid40900722,
year = {2025},
author = {Jones, OE and Beckett, H and Abraham, AJ and Makunga, NP and Midgley, GF},
title = {Endozoochory by Black Rhinoceroses Enhances Germination of a Key Arid Savanna Tree Species.},
journal = {Ecology and evolution},
volume = {15},
number = {9},
pages = {e71951},
pmid = {40900722},
issn = {2045-7758},
abstract = {Megaherbivores are typically regarded as agents of top-down control, limiting woody encroachment through destructive foraging. Yet they also possess traits and engage in behaviours that facilitate plant success. For example, megaherbivores can act as effective endozoochorous seed dispersers. However, studies on facilitative roles are heavily biased towards the African savanna elephant (Loxodonta africana), with little attention paid to other species or to effects beyond germination, across early ontogenic stages. The African black rhinoceros (Diceros bicornis), an obligate browser that exhibits frugivory and defecates in fixed dung middens, may offer ecologically distinct dispersal services. We conducted controlled experiments to test whether black rhino interactions with Vachellia erioloba, a leguminous tree of ecological importance in arid savannas, enhance germination, early seedling development or seedling resilience to herbivory. Germination was compared among dung-derived seeds, untreated controls and chemically scarified seeds. Seedling growth was assessed in dung versus sand and under simulated black rhino herbivory. Dung-derived seeds germinated most steadily and produced the highest cumulative germination (+40%) over the longest period (+13 days). Growth trials revealed that dung substrates did not enhance initial growth. Rather, seedlings being older conferred greater resilience to biomass loss than exposure to different substrate conditions. Our results provide the first experimental evidence of an apparent mutualism between black rhino and V. erioloba. This relationship is not driven by enhanced seedling development through legacy effects of gut passage, nor by dung conditions, as expected. Instead, it stems from gut passage effects on germination. In addition to increasing total germination, gut passage accelerates germination and extends the germination period, producing a seedling cohort with both older individuals and greater age variation-a population structure that may enhance persistence beyond the germination bottleneck. This research supports a more nuanced view of megaherbivores as both disturbance agents and mutualists in arid ecosystems.},
}

@article {pmid40904111,
year = {2025},
author = {Kupczok, A and Gavriilidou, A and Paulitz, E and Guerrero-García, L and Baumdicker, F},
title = {Gene co-occurrence and its association with phage infectivity in bacterial pangenomes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240070},
pmid = {40904111},
issn = {1471-2970},
support = {//Deutsche Forschungsgemeinschaft/ ; },
mesh = {*Bacteriophages/physiology ; *Bacteria/genetics/virology ; *Genome, Bacterial ; Host Specificity ; *Genes, Bacterial ; Phylogeny ; },
abstract = {Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest. We recently developed Goldfinder, a phylogenetic method to discover gene co-occurrences across bacterial pangenomes. Here, we expand Goldfinder to infer which gene presences or absences influence bacterial sensitivity to phages. By integrating a bacterial pangenome with an experimentally determined host range matrix, we infer associations between phage infectivity and the presence of accessory genes in bacterial pangenomes. The presented approach can be applied to predict bacterial genes that potentially enable phage infection, bacterial genes that prevent phage infection, and potential interactions between particular bacterial and phage accessory genes. Finally, the predicted interactions are clustered and visualized with the software Cytoscape. Here, we present a method to identify candidate genes within the pool of mobile accessory genes that may contribute to phage-host interactions. This approach will help to set up follow-up experiments and to understand the complex interactions between phages and bacteria.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}

*Bacteriophages/physiology
*Bacteria/genetics/virology
*Genome, Bacterial
Host Specificity
*Genes, Bacterial
Phylogeny

@article {pmid40904416,
year = {2025},
author = {Hutchinson, F and Crowley, LM and Broad, GR and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown Moss-moth, Bryotropha terrella (Denis & Schiffermüller), 1775.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {310},
pmid = {40904416},
issn = {2398-502X},
abstract = {We present a genome assembly from a female specimen of Bryotropha terrella (Brown Moss-moth; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a total length of 756.35 megabases. Most of the assembly (99.62%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.29 kilobases.},
}

@article {pmid40904542,
year = {2025},
author = {Zhang, L and Xiong, A and Li, C and Liu, X and Zhang, X and Gong, S and Yan, M and Qin, X and Liu, Y and Hu, Z and Fang, JK and Duan, H and Liu, H and Chan, LL and Jin, LN},
title = {Ecological pattern of microalgal communities and associated risks in coastal ecosystems.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf109},
pmid = {40904542},
issn = {2730-6151},
abstract = {Eukaryotic harmful and toxic microalgae, along with their derived toxins, pose significant threats to seafood safety, human health, and marine ecosystems. Here, we developed a novel full-length 18S rRNA database for harmful and toxic microalgae and combined metabarcoding with toxin analyses to investigate the ecological patterns of phytoplankton communities and the underlying mechanism of associated toxic microalgae risks. We identified 79 harmful and toxic species in Hong Kong's coastal waters, with dinoflagellates and diatoms representing the majority of toxic and harmful taxa, respectively. Distinct seasonal succession patterns were observed in phytoplankton communities, driven by different ecological assembly processes. Deterministic processes dominated during the dry season, correlating with elevated toxic microalgae abundance and temperature stress. Seasonal shifts in temperature played a pivotal role in shaping toxic algal communities. The dominance of dinoflagellates, particularly Alexandrium spp., Dinophysis spp., Prorocentrum spp., and Karenia spp., during the dry season was consistent with elevated toxin concentrations. These toxin profiles highlight the heightened risk in a warming climate, where the prevalence and impacts of toxigenic algae are expected to intensify.},
}

@article {pmid40904625,
year = {2025},
author = {Hébert-Dufresne, L and Ahn, YY and Allard, A and Colizza, V and Crothers, JW and Dodds, PS and Galesic, M and Ghanbarnejad, F and Gravel, D and Hammond, RA and Lerman, K and Lovato, J and Openshaw, JJ and Redner, S and Scarpino, SV and St-Onge, G and Tangherlini, TR and Young, JG},
title = {One pathogen does not an epidemic make: a review of interacting contagions, diseases, beliefs, and stories.},
journal = {Npj complexity},
volume = {2},
number = {1},
pages = {26},
pmid = {40904625},
issn = {2731-8753},
support = {K23 AI175660/AI/NIAID NIH HHS/United States ; P20 GM125498/GM/NIGMS NIH HHS/United States ; },
abstract = {From pathogens and computer viruses to genes and memes, contagion models have found widespread utility across the natural and social sciences. Despite their success and breadth of adoption, the approach and structure of these models remain surprisingly siloed by field. Given the siloed nature of their development and widespread use, one persistent assumption is that a given contagion can be studied in isolation, independently from what else might be spreading in the population. In reality, countless contagions of biological and social nature interact within hosts (interacting with existing beliefs, or the immune system) and across hosts (interacting in the environment, or affecting transmission mechanisms). Additionally, from a modeling perspective, we know that relaxing these assumptions has profound effects on the physics and translational implications of the models. Here, we review mechanisms for interactions in social and biological contagions, as well as the models and frameworks developed to include these interactions in the study of the contagions. We highlight existing problems related to the inference of interactions and to the scalability of mathematical models and identify promising avenues of future inquiries. In doing so, we highlight the need for interdisciplinary efforts under a unified science of contagions and for removing a common dichotomy between social and biological contagions.},
}

@article {pmid40906521,
year = {2025},
author = {Selten, G and Gómez-Repollés, A and Lamouche, F and Radutoiu, S and de Jonge, R},
title = {SyFi: generating and using sequence fingerprints to distinguish SynCom isolates.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
pmid = {40906521},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; *Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; *DNA Fingerprinting/methods ; Sequence Analysis, DNA/methods ; },
abstract = {The plant root microbiome is a complex community shaped by interactions among bacteria, the plant host and the environment. Synthetic community (SynCom) experiments help disentangle these interactions by inoculating host plants with a representative set of culturable microbial isolates from the natural root microbiome. Studying these simplified communities provides valuable insights into microbiome assembly and function. However, as SynComs become increasingly complex to better represent natural communities, bioinformatics challenges arise. Specifically, accurately identifying and quantifying SynCom members based on, for example, 16S rRNA amplicon sequencing becomes more difficult due to the high similarity of the target amplicon, limiting downstream interpretations. Here, we present SynCom Fingerprinting (SyFi), a bioinformatics workflow designed to improve the resolution and accuracy of SynCom member identification. SyFi consists of three modules: the first module constructs a genomic fingerprint for each SynCom member based on its genome sequence and, when available, raw genomic reads, accounting for both copy number and sequence variation in the target gene. The second module extracts the target region from this genomic fingerprint to create a secondary fingerprint linked to the relevant amplicon sequence. The third module uses these fingerprints as a reference to perform pseudoalignment-based quantification of SynCom member abundance from amplicon sequencing reads. We demonstrate that SyFi outperforms standard amplicon analysis by leveraging natural intragenomic variation, enabling more precise differentiation of closely related SynCom members. As a result, SyFi enhances the reliability of microbiome experiments using complex SynComs, which more accurately reflect natural communities. This improved resolution is essential for advancing our understanding of the root microbiome and its impact on plant health and productivity in agricultural and ecological settings. SyFi is available at https://github.com/adriangeerre/SyFi.},
}

*Microbiota/genetics
*Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Computational Biology/methods
High-Throughput Nucleotide Sequencing
*DNA Fingerprinting/methods
Sequence Analysis, DNA/methods

@article {pmid40908443,
year = {2025},
author = {Kaplan, DM and Alvarez, SJA and Palitsky, R and Choi, H and Clifford, GD and Crozier, M and Dunlop, BW and Grant, GH and Greenleaf, MN and Johnson, LM and Maples-Keller, J and Levin-Aspenson, HF and Mascaro, JS and McDowall, A and Pozzo, NS and Raison, CL and Zarrabi, AJ and Rothbaum, BO and Lam, WA},
title = {Correction: Fabla: A voice-based ecological assessment method for securely collecting spoken responses to researcher questions.},
journal = {Behavior research methods},
volume = {57},
number = {10},
pages = {274},
doi = {10.3758/s13428-025-02818-9},
pmid = {40908443},
issn = {1554-3528},
}

@article {pmid40909344,
year = {2025},
author = {Polak, I and Stryiński, R and Paukszto, Ł and Jastrzębski, JP and Bogacka, I and Łopieńska-Biernat, E},
title = {Diversity, expression, and structural modeling of sugar transporters in Anisakis simplex s. s. L3 and L4 larvae: an in vitro and in silico study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1621051},
pmid = {40909344},
issn = {2235-2988},
mesh = {Animals ; Larva/genetics/metabolism ; *Anisakis/genetics/metabolism/growth & development ; *Glucose Transport Proteins, Facilitative/genetics/metabolism/chemistry ; Computer Simulation ; Computational Biology ; Glucose/metabolism ; Phylogeny ; *Monosaccharide Transport Proteins/genetics/metabolism/chemistry ; Biological Transport ; *Helminth Proteins/genetics/metabolism/chemistry ; Gene Expression Profiling ; Models, Molecular ; },
abstract = {INTRODUCTION: Glucose transporter (GLUT) research in parasitic nematodes focuses on identifying and characterizing developmentally regulated isoforms, elucidating their regulatory and structural properties, and evaluating their potential as drug targets. While glucose transport mechanisms have been well characterized in the free-living nematode Caenorhabditis elegans, data on parasitic species remain limited. Anisakis simplex s. s., a parasitic nematode, relies on host-derived glucose to maintain energy metabolism. It is hypothesized that A. simplex s. s. utilizes specific glucose transporters to facilitate sugar uptake under varying nutritional conditions.

MATERIALS AND METHODS: In silico analysis identified five putative facilitated glucose transporter genes (fgt-1, fgt-2, fgt-3, fgt-5, fgt-9) and one Sugars Will Eventually be Exported Transporter (sweet-1) gene. The FGTs were classified as members of the solute carrier family 2 (SLC2), while sweet-1 belonged to the SWEET transporter family. Full-length cDNA sequences were obtained, and encoded proteins structurally characterized using bioinformatic modeling. Expression of transporter genes was assessed in A. simplex s. s. larvae at stages L3 and L4 cultured in vitro under different glucose concentrations and time points.

RESULTS: Structural and phylogenetic analyses revealed that fgt-1 and fgt-3 share high similarity with class I GLUTs found in nematodes and vertebrates. Gene expression profiling demonstrated differential regulation between larval stages. Most notably, FGT genes were stably expressed in L4 larvae, whereas in L3 larvae, gene activation was more variable and dependent on glucose concentration, showing a dynamic transcriptional response to nutrient levels. Sweet-1 was expressed in both stages, but its regulation differed over time and with glucose availability. Glucose supplementation altered trehalose and glycogen levels, and trehalase activity varied across stages and treatments, indicating stage-specific metabolic adaptation.

DISCUSSION: The observed transcriptional and biochemical differences between L3 and L4 larvae suggest a shift in glucose uptake mechanisms, from transcuticular absorption in L3 to intestinal glucose uptake in L4 following intestine activation. FGT1 and FGT3 are proposed as key facilitators of glucose uptake, with roles varying across developmental stages. These findings indicate that glucose transporters are regulated in response to changing environmental conditions and may represent targets for rational anthelmintic drug design.},
}

Animals
Larva/genetics/metabolism
*Anisakis/genetics/metabolism/growth & development
*Glucose Transport Proteins, Facilitative/genetics/metabolism/chemistry
Computer Simulation
Computational Biology
Glucose/metabolism
Phylogeny
*Monosaccharide Transport Proteins/genetics/metabolism/chemistry
Biological Transport
*Helminth Proteins/genetics/metabolism/chemistry
Gene Expression Profiling
Models, Molecular

@article {pmid40910796,
year = {2025},
author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R},
title = {The Earth Hologenome Initiative: Data Release 1.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação/ ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; },
abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.

RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.

CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}

Animals
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
Earth, Planet
*Vertebrates/genetics/microbiology
Databases, Genetic

@article {pmid40911670,
year = {2025},
author = {Wan, N and Duan, Q and Cai, Z and Zhu, Z and Wang, J and Tian, Y and Shen, W and Li, B and Kuang, Z and Liang, X and Liu, S and An, X and Yang, X and Liu, X and Mao, L and Chen, J and Wang, Y and Feng, Z and Liu, W and Bu, Y and Nevo, E and Papa, R and Meyer, A and Liu, J and Li, K},
title = {Aplf/Dna2 variants drive chromosomal fission and accelerate speciation in zokors.},
journal = {Science advances},
volume = {11},
number = {36},
pages = {eadt2282},
pmid = {40911670},
issn = {2375-2548},
mesh = {Multiomics ; Chromosomes ; Animals ; *Rodentia/classification/genetics ; *DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; *DNA Helicases/genetics ; *Endodeoxyribonucleases/genetics ; Genome ; Molecular Sequence Annotation ; Synteny ; Genomic Structural Variation ; Genetic Speciation ; Genetics, Population ; Telomere ; Phylogeny ; Base Sequence ; Genetic Variation ; },
abstract = {Chromosomal fissions and fusions are common, yet the molecular mechanisms and implications in speciation remain poorly understood. Here, we confirm a fission event in one zokor species through multiple-omics and functional analyses. We traced this event to a mutation in a splicing enhancer of the DNA repair gene Aplf in the fission-bearing species, which caused exon skipping and produced a truncated protein that disrupted DNA repair. An intronic deletion in Dna2, known to facilitate neo-telomere formation when knocked out, reduced gene activity. These variants collectively drove chromosomal fission in this zokor species. The newly formed chromosome became fixed due to carrying essential genes and strong selective pressure. While geographic isolation likely initiated the divergence of this species and the sister one, the fission event and associated decline at the chromosome level in gene flow probably exacerbated the speciation process. Our work elucidates the genetic basis of chromosomal fission and underscores its role in speciation dynamics.},
}

Multiomics
Chromosomes
Animals
*Rodentia/classification/genetics
*DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics
*DNA Helicases/genetics
*Endodeoxyribonucleases/genetics
Genome
Molecular Sequence Annotation
Synteny
Genomic Structural Variation
Genetic Speciation
Genetics, Population
Telomere
Phylogeny
Base Sequence
Genetic Variation

@article {pmid40914230,
year = {2025},
author = {Xu, Y and Chevreul, K and Dindorf, C and Bismuth, É and Carel, JC and Michel, M},
title = {Association of socioeconomic status and hospital efficiency in Type-1 diabetic patients with ketoacidosis or diabetic coma: a secondary data analysis comparing nation-wide paediatric and adult admissions in France.},
journal = {Diabetes research and clinical practice},
volume = {229},
number = {},
pages = {112450},
doi = {10.1016/j.diabres.2025.112450},
pmid = {40914230},
issn = {1872-8227},
mesh = {Humans ; France/epidemiology ; *Diabetes Mellitus, Type 1/complications/economics/epidemiology/therapy ; Adult ; Male ; Female ; *Diabetic Ketoacidosis/economics/epidemiology/therapy ; Child ; Adolescent ; Length of Stay/statistics & numerical data/economics ; *Social Class ; Young Adult ; Middle Aged ; Child, Preschool ; *Diabetic Coma/economics/epidemiology/therapy ; *Hospitalization/statistics & numerical data/economics ; Secondary Data Analysis ; },
abstract = {AIMS: To study the association between socioeconomic status (SES) and hospital efficiency in Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma in mainland France, overall and in adults versus children.

METHODS: An observational study was carried out using exhaustive national hospital discharge databases. It included all admissions discharged from 2013 to 2019. SES was assessed using an ecological measure divided into national quintiles, and efficiency by variations in patients' length of stay (LOS) compared to mean national LOS and a comparison of production costs and revenues. Multilevel multivariable analyses were carried out to study the association.

RESULTS: 67,100 admissions were included. Multivariable analyses found a significant association between efficiency outcomes, SES and age. Compared to other age groups, children under 5 had higher LOS than the national mean and incurred higher costs than what hospitals were paid regardless of SES. In adults, there was a significant interaction between SES and age group, leading to significantly increased LOS and costs in adults from intermediate and/or lower SES groups.

CONCLUSIONS: Current payment methods using diagnosis-related groups may not adequately reflect the burden of Type 1 diabetes mellitus patients admitted for ketoacidosis or diabetic coma on hospitals.},
}

Humans
France/epidemiology
*Diabetes Mellitus, Type 1/complications/economics/epidemiology/therapy
Adult
Male
Female
*Diabetic Ketoacidosis/economics/epidemiology/therapy
Child
Adolescent
Length of Stay/statistics & numerical data/economics
*Social Class
Young Adult
Middle Aged
Child, Preschool
*Diabetic Coma/economics/epidemiology/therapy
*Hospitalization/statistics & numerical data/economics
Secondary Data Analysis

@article {pmid40915583,
year = {2026},
author = {Zhang, Y and Wang, B and Hassan, M and Zhang, X},
title = {Biochar-calcium alginate composite immobilizing Pseudomonas sp. H6 for phosphate and ammonium recovery: Multi-omics insights and practical application evaluation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133274},
doi = {10.1016/j.biortech.2025.133274},
pmid = {40915583},
issn = {1873-2976},
mesh = {*Alginates/chemistry ; *Charcoal/chemistry ; *Ammonium Compounds/isolation & purification ; *Phosphates/isolation & purification ; *Pseudomonas/metabolism ; Wastewater/chemistry ; Glucuronic Acid/chemistry ; Hexuronic Acids/chemistry ; Cells, Immobilized/metabolism ; Adsorption ; Water Purification/methods ; Biodegradation, Environmental ; Water Pollutants, Chemical/isolation & purification ; Multiomics ; },
abstract = {Water eutrophication has emerged as a pervasive ecological challenge worldwide. To realize the resource utilization of waste and nutrients, a novel rape straw-derived biochar-calcium alginate composite (M-CA-RBC) immobilized Pseudomonas sp. H6 was synthesized to simultaneously remove phosphate (PO4[3-]) and ammonium (NH4[+]) from distillery wastewater. The removal performance of PO4[3-] and NH4[+] by M-CA-RBC were investigated. The removal mechanisms were explored by using different adsorption models combined with microbial degradation kinetics, analysis of dissolved organic matter components, electrochemical analysis, metagenomics, and metabolomics. The resource application potential of M-CA-RBC was evaluated. The results showed that M-CA-RBC had good removal performance for PO4[3-] (17.81 mg/g) and NH4[+] (25.78 mg/g). Surface precipitation, electrostatic attraction, Poly-P accumulation, microbial-induced calcium precipitation, and microbial assimilation were the main removal mechanisms of PO4[3-] by M-CA-RBC. The removal mechanisms of NH4[+] were micropore filling, ion exchange, electrostatic attraction, and heterotrophic nitrification-aerobic denitrification (HN-AD). M-CA-RBC had a good application potential in the practical distillery wastewater, with removal rates of PO4[3-] and NH4[+] reaching 88% and 65%, respectively. After adsorption saturation, M-CA-RBC exhibited good stability, which could be used as a slow-release fertilizer to promote the growth of mung beans. This study provides practical significance for the efficient removal and recovery of nitrogen and phosphorus in wastewater.},
}

*Alginates/chemistry
*Charcoal/chemistry
*Ammonium Compounds/isolation & purification
*Phosphates/isolation & purification
*Pseudomonas/metabolism
Wastewater/chemistry
Glucuronic Acid/chemistry
Hexuronic Acids/chemistry
Cells, Immobilized/metabolism
Adsorption
Water Purification/methods
Biodegradation, Environmental
Water Pollutants, Chemical/isolation & purification
Multiomics

@article {pmid40919732,
year = {2026},
author = {Milligan, PD and Rossiter, J and Zare, A and Palmer, TM and Lemboi, J and Mizell, GM and Mosiany, J and Riginos, C and Goheen, JR and Pringle, EG},
title = {Mutualism, herbivory, and invasive ants as seasonally dependent drivers of root surface area in a foundational savanna ant-plant.},
journal = {The New phytologist},
volume = {249},
number = {2},
pages = {777-791},
doi = {10.1111/nph.70553},
pmid = {40919732},
issn = {1469-8137},
support = {1556905//Division of Environmental Biology/ ; 1935498//Division of Environmental Biology/ ; 2010075//National Science Foundation Division of Biological Infrastructure/ ; },
mesh = {Animals ; *Acacia/growth & development ; *Ants ; Convolutional Neural Networks ; Grassland ; *Herbivory ; *Introduced Species ; Mammals ; Models, Biological ; *Plant Roots/growth & development ; Rain ; Seasons ; *Symbiosis ; *Myrmecophytes/growth & development ; },
abstract = {Many plants are defended from herbivory by costly insect mutualists. Understanding positive associations between plants and mutualists requires a whole-plant perspective including roots. We hypothesized that root surface area increases with mutualist activity (to a saturation threshold) and recent rainfall but that this relationship shifts when herbivores are excluded. We also hypothesized that invasive ants limit root surface area and that mutualism breakdown driven by invaders blunts root responses to rainfall and herbivore exclusion. Using minirhizotrons (est. 2021), we surveyed root surface area of ant-acacias during a dry (2022) and then a wet (2023) season. Study plots either excluded or permitted vertebrate browsers, within a natural experiment comparing mutualist-defended ant-acacias to those invaded by a mutualism-disrupting ant. Root area increased with mutualist activity to a threshold, but this positive association was less apparent during rainy periods. Megabrowser exclusion increased overall root area but reduced the threshold for a positive association with mutualist activity and reduced the steepness of the root area-rainfall correlation. Ant-invaded acacias had smaller root areas that correlated less steeply with rainfall. Positive associations between insect defense and root area were thus contingent on rainfall, herbivory, and biotic invasion, drivers that are shifting under global change.},
}

Animals
*Acacia/growth & development
*Ants
Convolutional Neural Networks
Grassland
*Herbivory
*Introduced Species
Mammals
Models, Biological
*Plant Roots/growth & development
Rain
Seasons
*Symbiosis
*Myrmecophytes/growth & development

@article {pmid40920239,
year = {2026},
author = {Kröger, K and Wiemes, K and Santosa, F and Böhner, H and Lax, H and Stolpe, S and Kowall, B and Stang, A},
title = {Prescription of lipid-lowering drugs and their association with hospitalization for ST-elevation myocardial infarction (STEMI) in Germany in 2010-2022.},
journal = {Clinical research in cardiology : official journal of the German Cardiac Society},
volume = {115},
number = {2},
pages = {313-321},
pmid = {40920239},
issn = {1861-0692},
mesh = {Humans ; Germany/epidemiology ; *ST Elevation Myocardial Infarction/epidemiology/therapy ; *Hospitalization/trends/statistics & numerical data ; Male ; *Hypolipidemic Agents/therapeutic use ; Female ; Aged ; Middle Aged ; *Drug Prescriptions/statistics & numerical data ; },
abstract = {OBJECTIVES: We investigated changes in lipid-lowering drug prescriptions in Germany as a whole and in the 16 federal states over the last 13 years and their association with hospitalization rates for acute myocardial infarction.

DESIGN: Ecological study.

SETTING: Nationwide German hospitalization, Diagnosis-Related Groups Statistic.

PATIENTS/PARTICIPANTS: German population in the years 2010 through 2022.

INTERVENTION: All prescriptions of lipid-lowering drugs in the years 2010 to 2022 by federal state in Germany.

MAIN OUTCOME MEASURES: Hospitalization rates for the treatment of transmural infarction per calendar year and federal state (STEMI = ST-elevation myocardial infarction).

RESULTS: The age-standardized prescription rates of lipid-lowering drugs per 1000 person-years increased from 77.4 in 2010 to 145.2 in 2022 (reference population: Germany 2011). Within the same period, the STEMI hospitalization rate per 100,000 person-years decreased from 143.7 to 100.1. Based on the prescription and hospitalization rates of the 16 federal states, it is shown that the STEMI hospitalization rate decreased the more the prescription rate of lipid-lowering drugs in a federal state increased over time (beta = 0.38, 95% confidence interval - 0.64; - 0.12; adjusted explained variance 0.362).

CONCLUSION: Increasing prescription rates of lipid-lowering drugs have correlated with decreasing rates of hospitalized cases for STEMI in Germany in the last decade.},
}

Humans
Germany/epidemiology
*ST Elevation Myocardial Infarction/epidemiology/therapy
*Hospitalization/trends/statistics & numerical data
Male
*Hypolipidemic Agents/therapeutic use
Female
Aged
Middle Aged
*Drug Prescriptions/statistics & numerical data