@article {pmid41034648,
year = {2025},
author = {Weingarten, A and Häusler, M and Serangeli, J and Verheijen, I and Reiter, E and Radzevičiūtė, R and Stoessel, A and Krause, J and Spyrou, MA and Conard, NJ and Nieselt, K and Posth, C},
title = {Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {41034648},
issn = {2397-334X},
abstract = {Deep-time palaeogenomics offers rare insights into macroevolutionary events for both extant and extinct species. Aside from a Middle Pleistocene genome from North American permafrost (780-560 ka) and a number of Late Pleistocene specimens, most ancient horse DNA studies have focused on tracing the origins of domestication and subsequent periods. Here we present mitochondrial genomes from two Equus mosbachensis specimens from Schöningen, Germany, a Middle Pleistocene archaeological site complex with direct and repeated evidence of hominin-horse interactions on the shore of a palaeolake. Using petrous bone sampling, targeted enrichment and damage-aware and polarization-free mitochondrial DNA reconstruction methods, we extend the range of genome recovery in open-air sites to ~300,000 years ago. Phylogenetic analyses position these mitochondrial DNAs in two distinct, deeply divergent lineages, basal to both previously sequenced ancient Eurasian specimens and all modern-day horses. The Schöningen horse mitochondrial DNA data reveal a previously unrecognized diversification event within the clade, ultimately giving rise to modern-day horses, that is molecularly dated to ~570 ka and provides genetic support for the morphological species assignment. By extending the recoverable limits of ancient DNA from Middle Pleistocene open-air sites, our molecular findings bridge a temporal and geographic gap, providing insights on early evolutionary events within the genus Equus.},
}

@article {pmid41032589,
year = {2025},
author = {Yang, M and Adegbite, O and Chang, P and Cheng, J and Wang, Y and Held, M and Zhu, X and Li, Y and Dykes, GF and Chen, Y and Savage, N and Zhang, YZ and Gao, J and Hinton, JCD and Lian, LY and Liu, LN},
title = {Molecular basis of the biogenesis of a protein organelle for ethanolamine utilization.},
journal = {Science advances},
volume = {11},
number = {40},
pages = {eadx9774},
doi = {10.1126/sciadv.adx9774},
pmid = {41032589},
issn = {2375-2548},
mesh = {*Ethanolamine/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Organelles/metabolism ; *Salmonella/metabolism ; },
abstract = {Many pathogenic bacteria use proteinaceous ethanolamine utilization microcompartments (Eut BMCs) to catabolize ethanolamine. This ability gives pathogens a competitive edge over commensal microbiota, which can drive virulence in the inflamed gut. Despite such a critical function, the molecular mechanisms underlying the synthesis of Eut BMCs remain elusive. We report a systematic study for dissecting the molecular basis underlying Eut BMC assembly in Salmonella. We determined the functions of individual constituent proteins in the structure and function of Eut BMCs and demonstrated that EutQ is essential for cargo encapsulation and Eut BMC formation through specific association with the shell and cargo enzymes. We found that Eut proteins can self-assemble to form cargo and shell aggregates independently in vivo and that the biogenesis of Eut BMCs follows a "shell-initiated" pathway. Cargo enzymes exhibit dynamic liquid-like organization within the Eut BMC. Our findings provide mechanistic insights into the structure and assembly of the Eut BMC that serves as a paradigm for membraneless organelles.},
}

*Ethanolamine/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
*Organelles/metabolism
*Salmonella/metabolism

@article {pmid41032510,
year = {2025},
author = {Zhang, C and Teng, J and Liu, P and Liu, C},
title = {Ecological suitability evaluation of traditional village locations in Jiangxi Province based on multi-model integration using artificial intelligence.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332375},
doi = {10.1371/journal.pone.0332375},
pmid = {41032510},
issn = {1932-6203},
mesh = {*Artificial Intelligence ; China ; *Ecosystem ; Humans ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Neural Networks, Computer ; *Ecology ; Support Vector Machine ; },
abstract = {Traditional villages have evolved over time to adapt to their environmental characteristics, demonstrating high ecological suitability. Ideal village locations not only provide comfortable living spaces but also ensure safety and sustainability, reflecting the ancestors' profound understanding of the natural environment and ecological wisdom. This study employs an artificial intelligence-based multi-model integration approach to evaluate the ecological suitability of 413 traditional village sites in Jiangxi Province. Key influencing factors are identified, and the ecological wisdom of ancestral site selection is analyzed, resulting in an ecological suitability evaluation map for traditional village locations in Jiangxi Province. The study draws upon environmental characteristic data of Jiangxi Province, including topography, climate, habitat quality, land use, air quality, vegetation cover, and river network density. GIS technology is utilized for spatial analysis and result visualization, with raster data being extracted and standardized. Machine learning methods, such as Random Forest, Support Vector Machine, and Gradient Boosting Decision Trees, along with deep learning methods like Convolutional Neural Networks and Multilayer Perceptrons, are applied. Multi-model integration techniques combine diverse predictive outputs, thereby enhancing the overall accuracy and robustness of ecological suitability evaluations. Experimental results indicate that elevation, slope, habitat quality, actual distance to water bodies, and average temperature are the main influencing factors for village site selection. The multi-model integration method performs excellently in evaluating ecological suitability, effectively identifying key ecological factors. The model's accuracy and reliability are verified through confusion matrix, feature importance analysis, and ROC curve. By analyzing the impact weights of various ecological factors, this study constructs a Composite Suitability Index (CSI) and generates an ecological suitability evaluation map that clearly displays suitability levels. This provides a scientific basis for the protection and rational development of traditional villages and serves as a reference for ecological site selection studies in other regions.},
}

*Artificial Intelligence
China
*Ecosystem
Humans
*Conservation of Natural Resources/methods
Geographic Information Systems
Neural Networks, Computer
*Ecology
Support Vector Machine

@article {pmid41030122,
year = {2025},
author = {Robinson, JM and Brame, J and Cando-Dumancela, C and Deshmukh, S and Fickling, NW and Hawken, S and Hayward, C and Kuhn, E and Lee, K and Liddicoat, C and Ramesh, S and Robinson, K and Sun, X and Breed, MF},
title = {Mapping and Cataloguing Microbial and Biochemical Determinants of Health: Towards a 'Database of Salutogenic Potential'.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70243},
doi = {10.1111/1751-7915.70243},
pmid = {41030122},
issn = {1751-7915},
support = {//National Environmental Science Program/ ; 32361143523//National Natural Science Foundation of China/ ; UOWX2101//New Zealand Ministry of Business Innovation and Employment/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; 2023YFF1304600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Environmental Microbiology ; *Databases, Factual ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Microbial and biochemical research has historically focused on pathogenic agents due to their clear association with disease. This is a perspective that has saved countless lives but encourages a skewed, threat-centered view of microbes and biogenic compounds. Emerging evidence shows that exposure to diverse environmental microbiomes and natural biochemical products is also salutogenic-promoting health and resilience. Here we introduce the 'Database of Salutogenic Potential', a prototype relational repository cataloguing environmental microbes and biochemical compounds linked to health benefits. Drawing from more than 200 articles, we identified 124 potentially salutogenic microbial taxa, 14 biochemical compounds and 63 associated benefits. By creating a structured and open platform, we aim to shift the balance between pathogen-centric and salutogenic perspectives, potentially enabling future applications in public health, urban planning and ecosystem restoration. While the current iteration of the database primarily centers on human health outcomes, it is designed to expand into ecosystem health domains, embedding salutogenic thinking into One Health frameworks. We present this as a first step, not a ready-to-use tool, and invite collaborative refinement from the scientific community.},
}

Humans
*Microbiota
*Environmental Microbiology
*Databases, Factual
*Bacteria/metabolism/classification/genetics

@article {pmid41029229,
year = {2025},
author = {Nagy, KN and Károlyi, CE and Bakacsy, L},
title = {Multiscale assessment of conservation management for Amorpha fruticosa invasion in a marsh meadow.},
journal = {BMC ecology and evolution},
volume = {25},
number = {1},
pages = {97},
pmid = {41029229},
issn = {2730-7182},
support = {7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; 7616//University of Szeged Open Access Found/ ; },
mesh = {*Introduced Species ; *Wetlands ; *Conservation of Natural Resources/methods ; Biodiversity ; Animals ; Cattle ; *Fabaceae/physiology ; },
abstract = {This study examined the ecological impact of the invasive shrub Amorpha fruticosa in marsh meadows and assessed the effectiveness of combined conservation management practices, i.e., mowing and cattle grazing, in on restoring native vegetation. Conducted in the Mártély Landscape Protection Area (Hungary), the research used a multiscale approach to compare treated non-invaded and treated invaded wetland vegetation. Information theory-based diversity metrics were employed to evaluate the impact of A. fruticosa on structural complexity and species composition. Results revealed that although A. fruticosa can significantly altered plant community structure, the implemented management strategies effectively reduced its impact. The treated invaded vegetation exhibited diversity levels compareable to native marshland communities, suggesting that mowing and grazing contributed to decreasing A. fruticose dominance. However, in the absence of untreated control stands, this pattern must be interpreted cautiously, as the observed similarity could be conclusively attributed to the applied management alone. A slight, but non-significant shift in structural diversity was also observed, implying a residual effect of invasion. This study underscores the value of active, combined conservation strategies in maintaining biodiversity and ecosystem resilience in wetland habitats. The results contribute to broader discussions on invasive species control, emphasizing the role of traditional land-use practices in mitigating the ecological effects of biological invasions.},
}

*Introduced Species
*Wetlands
*Conservation of Natural Resources/methods
Biodiversity
Animals
Cattle
*Fabaceae/physiology

@article {pmid41028195,
year = {2025},
author = {Yang, M and Wang, M and Cao, L and Zhang, H},
title = {Integrating trade-offs and supply-demand into ecosystem service zoning management to provide more targeted management strategies from the water-food-ecosystem nexus perspective.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33957},
pmid = {41028195},
issn = {2045-2322},
support = {42401384//National Natural Science Foundation of China/ ; 41971241//National Natural Science Foundation of China/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 24YJCZH376//Humanities and Social Sciences Youth Foundation, Ministry of Education/ ; 25IRTSTHN008//Higher Education Institutions Scientific and Technological Innovation Team Support Program in Henan Province/ ; 25A170008//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; 24B170003//Key Scientific Research Projects of Colleges and Universities in Henan Province/ ; },
abstract = {The water-food-ecosystem nexus (WFE nexus) forms the foundation for achieving sustainable development. Managing ecosystem services (ESs) from this perspective is crucial for maintaining and enhancing ecosystem sustainability. However, synchronously mitigating trade-offs and supply-demand conflicts among ESs poses a significant challenge for sustainable ecosystem management. This study proposes a spatial management zoning framework integrating information on ESs trade-offs and supply-demand relationships from the perspective of the WFE nexus. This framework aims to precisely distinguish regional differences in ESs trade-off characteristics and supply-demand risk levels. We applied this framework to China's Loess Plateau (LP) in China, where the simultaneous safeguarding of water, food, and ecological security has become a major challenge for local sustainable development. Based on analyzing ESs trade-offs and supply-demand matching relationships, our framework divided the LP into ten management zones. Each of these zones faces similar ecological issues internally, while different zones confront distinct ecological problems. Consequently, we propose targeted management strategies for each zone based on their unique ecological issues. Our framework deepens the research on the WFE nexus and provides a new perspective for simultaneously resolving ESs trade-offs and supply-demand conflicts.},
}

@article {pmid41026600,
year = {2025},
author = {Liu, L and Han, P and Wang, J and Xiuqin, S and Xu, G and Wang, L and Liu, R and Shen, X and Chen, F},
title = {Approaches to the water environment and aquatic ecology governance in basin systems.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {6},
pages = {894-902},
pmid = {41026600},
issn = {0273-1223},
support = {ZR2024MD117//Natural Science Foundation of Shandong Province/ ; No.0031504//The Shandong Top Talent Special Foundation/ ; X20192Z//The Doctoral research fund project of Shandong Jianzhu University/ ; 42107496//The National Science Fund for Distinguished Young Scholars-Construction and application of remote sensing ecological index model of Tamarix shrubbery forest/ ; },
mesh = {*Ecology ; *Conservation of Natural Resources ; Ecosystem ; Sustainable Development ; },
abstract = {With the development of human civilization and the rapid progress of urbanization, the water environment and aquatic ecology need more systematic treatment to support the construction of ecological civilization and sustainable development. Based on a large number of research results and from the four dimensions including governance concept, governance technology, management and control platform and engineering strategy suggestions, this study systematically analysed the cutting-edge concepts such as reverse-driven governance, explored the application of key technologies such as remote sensing in the water environment and water ecological governance, put forward strategic suggestions on building an intelligent analysis and decision-making platform and avoiding great leap forward-style vanity projects in the water environment and aquatic ecology governance. Finally, six cutting-edge governance concepts, four key technologies, two types of governance and control platforms and two engineering strategies were sorted out and formed a governance system covering concept guidance, technical support, platform integration and application, and engineering strategy guarantee. The research enriches the theory of the water environment and aquatic ecology governance, and has important reference value for policy-making and engineering practice of watershed water environment and aquatic ecology governance.},
}

*Ecology
*Conservation of Natural Resources
Ecosystem
Sustainable Development

@article {pmid41021230,
year = {2025},
author = {Muzekari, B and Cooper, N and Resnick, A and Paul, AM and Torres-Grillo, OE and Andrews, ME and Mattan, B and Scholz, C and Johnson, D and Carreras-Tartak, J and Cakar, ME and Hao, S and Zhou, E and Beard, E and Mesquiti, S and Sayed, F and Fichman, MA and Lydon-Staley, DM and Barnett, IJ and Strasser, AA and Kirchner, TR and Henriksen, L and Falk, EB},
title = {Naturalistic Tobacco Retail Exposure and Smoking Outcomes in Adults Who Smoke Cigarettes Daily.},
journal = {JAMA network open},
volume = {8},
number = {9},
pages = {e2530132},
doi = {10.1001/jamanetworkopen.2025.30132},
pmid = {41021230},
issn = {2574-3805},
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; *Tobacco Products/economics/statistics & numerical data ; Craving ; *Commerce/statistics & numerical data ; Aged ; *Cigarette Smoking/epidemiology/psychology ; Cohort Studies ; Young Adult ; Ecological Momentary Assessment ; New Jersey/epidemiology ; *Tobacco Industry ; },
abstract = {IMPORTANCE: The tobacco industry spends more than $8 billion annually in the US on marketing at the point of sale. Exposure to tobacco retail has been associated with smoking outcomes, but substantially less is known about how objectively logged everyday tobacco retail exposure is associated with smoking outcomes.

OBJECTIVE: To assess preregistered hypotheses that individuals would report (1) greater craving and (2) more cigarettes smoked on days when their exposure to tobacco retail is higher than usual.

This multimodal, within-person cohort study combined objectively logged geolocation tracking, public tobacco retail location records, and ecological momentary assessment data. Eligible participants recruited from the GeoSmoking Study were aged 21 to 65 years, smoked at least 5 cigarettes per day over the previous 6 months, owned a smartphone, and were a resident of Pennsylvania, New Jersey, or Delaware. Data were collected from May 25, 2022, to June 10, 2024.

EXPOSURE: Exposure to tobacco retail stores was assessed using mobility data matched with locations of tobacco retailers across Pennsylvania, New Jersey, and Delaware.

MAIN OUTCOMES AND MEASURES: Daily mean craving and daily number of cigarettes smoked were computed using ecological momentary assessment.

RESULTS: A total of 273 participants were included in the final analyses (mean [SD] age, 42.5 [10.7] years; 151 women [55.3%]). Multilevel models revealed support for both preregistered hypotheses. On days when individuals had more tobacco retail exposure than their own average, they reported significantly higher levels of craving (b = 0.04; 95% CI, 0.01-0.07; t3457 = 2.72; P = .01) and smoking significantly more cigarettes (b = 0.01; 95% CI, 0.0002-0.01; t3469 = 2.05; P = .04).

CONCLUSIONS AND RELEVANCE: In this cohort study of individuals who smoke cigarettes daily, exposure to tobacco retail in their everyday lives was associated with increases in craving and smoking. These findings highlight the importance of retail exposure and smoking outcomes, information that is critical for developing effective tobacco control interventions and lays the foundation for broader health research on environmental factors that shape health behaviors.},
}

Humans
Female
Male
Adult
Middle Aged
*Tobacco Products/economics/statistics & numerical data
Craving
*Commerce/statistics & numerical data
Aged
*Cigarette Smoking/epidemiology/psychology
Cohort Studies
Young Adult
Ecological Momentary Assessment
New Jersey/epidemiology
*Tobacco Industry

@article {pmid41020379,
year = {2025},
author = {Vázquez, E and Duong, I and Rabin, BA and Stadnick, NA and Watson, PL and Cain, KL and Pozar, M and Cheney, A},
title = {Ripple Effects Mapping: Evaluating Multilevel Perspectives and Impacts of a Statewide Community-Academic Partnership Network on Covid-19 Health Disparities.},
journal = {Health expectations : an international journal of public participation in health care and health policy},
volume = {28},
number = {5},
pages = {e70446},
doi = {10.1111/hex.70446},
pmid = {41020379},
issn = {1369-7625},
support = {//This paper was supported by the following funding NIH/NHLBI CEAL grant #21-312-0217571-66106L./ ; },
mesh = {Humans ; *COVID-19/epidemiology/ethnology ; *Health Status Disparities ; California/epidemiology ; Community-Based Participatory Research ; *Community-Institutional Relations ; Universities/organization & administration ; *Community Networks/organization & administration ; SARS-CoV-2 ; Female ; },
abstract = {INTRODUCTION: Community-academic partnerships played an important role in addressing Covid-19-related health disparities in historically marginalised groups such as racial ethnic minorities and low-income and rural communities in the pandemic. Part of the federal response involved establishing regional community academic networks that engaged highly impacted communities in health disparities research. The statewide Share, Trust, Organize, Partner COVID-19 California Alliance (STOP COVID-19 CA) network was part of the federal response.

METHODS: In spring 2024, ripple effects mapping (REM), a participatory action research method, was used to conduct an evaluation of the impact of the STOP COVID-19 network on the capacity of community-academic partnerships to carry out Covid-19-related health disparities research. This method uses group interviews to capture direct and indirect outcomes, that is, ripples, of community-based programmes. Short-, medium- and long-term changes and conditions related to community-academic partnerships in the statewide network were mapped onto the spheres of influence of the social ecological model.

RESULTS: A total of 24 participants took part in one of three REM sessions. Community and academic partners were represented in all sessions, and most had been involved in community-engaged research for 3 to 10+ years. Most identified as female, Hispanic/Latino, and between the ages of 40 and 49. Qualitative analysis of sessions indicated that most changes occurred at the individual and interpersonal levels and involved medium-term changes (e.g., increased capacity to partner in research and shared understanding). Neighbourhood- or community-level changes included identification of culturally and linguistically responsive intervention and dissemination efforts (e.g., promotora model). Policy and built environment conditions reveal the inequities in higher education and the need for structural-level changes to university infrastructure and grant administration.

CONCLUSION: Most outcomes were observed at the individual and interpersonal (group) levels and involved primarily medium-term changes. However, the network itself served as a platform to discuss the need for structural-level changes within university infrastructure to facilitate community-engaged scholarship. Such networks have the potential to facilitate capacity building for community-academic partnerships to collaborate in health disparities research that can generate evidence to move forward public health policy change.

Community partners, including grassroots leaders and staff of community-based organisations, were involved in the development of the research questions, the design of the study, and data collection, analysis and interpretation of the findings. Community partners also contributed to manuscript development.},
}

Humans
*COVID-19/epidemiology/ethnology
*Health Status Disparities
California/epidemiology
Community-Based Participatory Research
*Community-Institutional Relations
Universities/organization & administration
*Community Networks/organization & administration
SARS-CoV-2
Female

@article {pmid41016700,
year = {2025},
author = {Albertina, EA and Torres, L and Sauber, G and Hillard, CJ and Fitzgerald, JM and deRoon-Cassini, TA and Larson, CL},
title = {Endocannabinoids Mediate Racial/Ethnic Discrimination Prediction of Post-Traumatic Stress Disorder Symptoms Moderated by Resting-State Functional Connectivity in Black and African American Individuals.},
journal = {Biological psychiatry. Cognitive neuroscience and neuroimaging},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bpsc.2025.09.016},
pmid = {41016700},
issn = {2451-9030},
abstract = {BACKGROUND: Individuals from marginalized ethnoracial groups face higher risk for posttraumatic stress disorder (PTSD) symptoms, exacerbated by experiencing racial/ethnic discrimination. Prior work separately explored the endocannabinoid (eCB) system and functional connectivity response to stress/trauma, and suggests that experiences of chronic minority stress, such as racial discrimination, contribute to eCB tone and resting state functional connectivity. We explored how circulating eCB tone, in conjunction with resting-state connectivity, contributes to increased risk for PTSD symptoms following trauma among individuals experiencing discrimination.

METHODS: Black/African Americans (n=74, Mage=33.81) were recruited from a Level 1 trauma center. Correlational and linear models explored whether experiences of racial/ethnic discrimination (PEDQ), eCB (AEA, 2-AG) concentrations, default mode network (DMN), or salience network (SN) functional connectivity were associated with PTSD symptoms (PCL-5). We then explored moderated mediation models where discrimination predicted PTSD symptoms with eCB concentration as a mediator and functional connectivity as a moderator.

RESULTS: Discrimination was correlated with PTSD symptoms (r=0.50), serum AEA concentration (r=0.43), and DMN connectivity (r=0.23). When including urine THC, lifetime trauma, age, and sex as covariates, AEA concentration was associated with PTSD symptoms (r=0.30) and DMN connectivity (r=0.24). AEA mediated the relationship between discrimination and PTSD symptoms, and SN connectivity moderated this mediation (B=52.46).

CONCLUSIONS: Our findings highlight how racial/ethnic discrimination impacts neurobiological systems that may lead to increased vulnerability for PTSD symptoms following an injury. Future work should continue to explore biological factors associated with the social-ecological model of health as mechanisms of risk for adverse outcomes following trauma.},
}

@article {pmid41013991,
year = {2025},
author = {Formanack, A and Ogle, K and Peltier, D},
title = {Flashy, decoupled, or declining? Single theories fail to explain the diversity of drought mortality signals in tree rings.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70605},
pmid = {41013991},
issn = {1469-8137},
abstract = {Growth patterns recorded in tree rings may predict drought 'winners' and 'losers'. Past studies of drought-killed trees have produced conflicting evidence. Some show killed trees were highly responsive to climate, while others suggest killed trees were climate-insensitive or became less sensitive over time. We leveraged ring width data from 2934 drought-killed and -surviving trees of seven species to compute growth sensitivity to seasonal climate variables via a Bayesian mixed effects model. Aided by clustering analyses, we evaluated how species conformed to three alternative hypotheses (theories): relative to surviving trees, killed trees (H1) have 'flashy' climate responses, (H2) are 'decoupled' from climate, or (H3) have 'declining' sensitivity over time. Differences in growth patterns were not consistent across species or status (surviving/killed). Drought-killed subalpine fir and Engelmann spruce exhibited 'flashy' growth - higher sensitivity of growth to climate over time - compared with survivors. Drought-killed aspen, Scots pine, and Norway spruce showed stable, climate-insensitive growth compared with survivors, suggesting 'decoupling' from climate. Most species showed nonstationary sensitivities, but rather than declining, some sensitivities increased, even in surviving trees. Our flashy-decoupled-declining framework links predictions for future drought-induced mortality to potential mechanisms, enhancing ecological and physiological understanding of growth-climate patterns preceding drought mortality events.},
}

@article {pmid41013625,
year = {2025},
author = {Li, M and Yang, H},
title = {Exploring spatial-temporal heterogeneity in new-type urbanization's impact on health expenditure: a GTWR analysis.},
journal = {International journal of health geographics},
volume = {24},
number = {1},
pages = {26},
pmid = {41013625},
issn = {1476-072X},
mesh = {Humans ; *Urbanization/trends ; *Health Expenditures/trends/statistics & numerical data ; China/epidemiology ; *Spatio-Temporal Analysis ; *Geographic Information Systems/trends ; },
abstract = {BACKGROUND: To address challenges arising from rapid urban development, China has formulated and implemented the New-Type Urbanization strategy. However, empirical research on the specific impacts between New-Type Urbanization and health expenditures remains limited.

METHODS: Using panel data from 31 Chinese provinces (2012-2019), this study constructed a comprehensive evaluation index system for New-Type Urbanization across four dimensions: demographic, economic, social, and ecological. Geographically and Temporally Weighted Regression was employed to examine the spatial effects, influencing factors, and spatial heterogeneity of New-Type Urbanization's impact on health expenditures.

RESULTS: The results show that China's health expenditures primarily exhibit High-High and Low-Low clustering patterns with spatial fluctuations. Meanwhile, the impact of New-Type Urbanization on health expenditures demonstrates spatiotemporal heterogeneity and non-stationarity. As urbanization levels increase, the negative effects of health expenditure clustering expand, while the influence of economic urbanization weaken.

CONCLUSIONS: Our findings fill the research gap regarding the impacts between New-Type Urbanization and health expenditures, while also providing direction for New-Type Urbanization development to support the implementation of health policies aimed at controlling health expenditure growth.},
}

Humans
*Urbanization/trends
*Health Expenditures/trends/statistics & numerical data
China/epidemiology
*Spatio-Temporal Analysis
*Geographic Information Systems/trends

@article {pmid41011672,
year = {2025},
author = {Song, C and Yan, M and Lin, S and Li, J and Zou, H and Hu, Z and Yan, X},
title = {Dual-Ionization SPME-GC-HRMS Metabolomic Profiling of Broccoli Volatiles for the Construction of a Broccoli Metabolic Database.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {18},
pages = {},
doi = {10.3390/molecules30183781},
pmid = {41011672},
issn = {1420-3049},
support = {2022YFE0108300//National Key R&D Program of China/ ; N20220013//the Basic Agricultural Research Project of Wenzhou/ ; },
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; *Brassica/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry/methods ; *Metabolomics/methods ; Solid Phase Microextraction/methods ; *Metabolome ; Principal Component Analysis ; Databases, Factual ; },
abstract = {Volatile organic compounds (VOCs) play critical roles in broccoli's sensory attributes, defense mechanisms, and ecological interactions, yet comprehensive profiling of its volatilome remains limited. This study aimed to construct a robust and inclusive volatile metabolite database for broccoli using advanced analytical techniques. A pooled sample comprising florets from 191 cultivars was prepared to capture broad chemical diversity and analyzed using solid-phase microextraction-gas chromatography-high-resolution mass spectrometry (SPME-GC-HRMS) under dual ionization modes: electron ionization (EI) and chemical ionization (CI). A total of 206 VOCs spanning nine chemical classes were detected, with 37 compounds further confirmed through synchronized CI analysis. To validate the database, broccoli florets from seven distinct cultivars were analyzed using the same workflow. Of the 206 compounds, 187 (90.78%) were detected in at least one cultivar, while 38 were consistently found across all samples, indicating a conserved core volatilome. Principal component analysis revealed distinct VOC profiles among cultivars, and freeze-dried samples were found suitable for reproducible large-scale analysis. This study demonstrates that a pooled-sample strategy coupled with dual-ionization GC-HRMS provides comprehensive and reliable VOC coverage. The resulting database offers a valuable resource for metabolomics studies in Brassica, with applications in cultivar differentiation, flavor research, and environmental response profiling.},
}

*Volatile Organic Compounds/analysis/metabolism/chemistry
*Brassica/metabolism/chemistry
Gas Chromatography-Mass Spectrometry/methods
*Metabolomics/methods
Solid Phase Microextraction/methods
*Metabolome
Principal Component Analysis
Databases, Factual

@article {pmid41009797,
year = {2025},
author = {Cheng, L and Shi, N and Du, X and Huang, T and Zhang, Y and Zhao, C and Zhao, K and Lin, Z and Ma, D and Li, Q and Wang, F and Yao, H and Shen, H},
title = {Bioinformatics Analysis and Expression Profiling Under Abiotic Stress of the DREB Gene Family in Glycyrrhiza uralensis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
doi = {10.3390/ijms26189235},
pmid = {41009797},
issn = {1422-0067},
support = {KY2025JBGS03//the Science and Technology Plan Project of the Third Division/ ; 32260083//the National Natural Science Foundation of China/ ; 2023AB052 and 2023CB008-17//a Science and Technology Project of Bingtuan/ ; RCZK202595//Scientific Research Startup Project for High-Level Talents, Shihezi University/ ; },
mesh = {*Gene Expression Regulation, Plant ; *Glycyrrhiza uralensis/genetics/metabolism ; *Stress, Physiological/genetics ; *Plant Proteins/genetics/metabolism ; *Computational Biology/methods ; Phylogeny ; *Transcription Factors/genetics/metabolism ; Gene Expression Profiling ; Droughts ; *Multigene Family ; Promoter Regions, Genetic ; Transcriptome ; },
abstract = {Glycyrrhiza uralensis is an important medicinal plant exhibiting strong tolerance to abiotic stresses, including drought and salinity. DREB (Dehydration-Responsive Element-Binding) transcription factors, key members of the AP2/ERF family, play crucial roles in plant growth, development, and stress responses. Based on transcriptome data, we identified 18 DREB transcription factors in G. uralensis, designated GuDREB1 to GuDREB18. Bioinformatics analysis revealed genomic sequences ranging from 534 to 2864 bp and coding sequence (CDS) lengths between 525 and 1509 bp. All GuDREB proteins contain a single AP2 domain, including the conserved YRG and RAYD elements, and were predicted to localize to the nucleus. Phylogenetic analysis clustered the G. uralensis DREBs with 61 Arabidopsis thaliana DREBs into five subgroups, indicating evolutionary conservation. Promoter analysis detected seventeen stress-responsive cis-acting elements, encompassing hormone-responsive and abiotic stress-responsive motifs, suggesting diverse biological functions. Tissue-specific expression profiling revealed GuDREB transcription in both aerial and underground parts. Drought stress induced varying degrees of GuDREB expression, confirming their involvement in stress responses. Notably, GuDREB10 expression increased significantly in underground parts, while GuDREB15 showed pronounced upregulation in aerial parts under drought; the GuDREB15 promoter contained the highest number of light-responsive elements (23), potentially explaining its aerial tissue specificity. Drought stress significantly increased abscisic acid (ABA) content. Underground parts exhibited higher initial sensitivity to drought, whereas aerial parts displayed a more sustained response; ABA levels overall showed an initial increase followed by a decline. This study expands the G. uralensis DREB gene database, provides a foundation for selecting stress-resistance genes, and offers insights into DREB functional roles in abiotic stress responses in this key medicinal species.},
}

*Gene Expression Regulation, Plant
*Glycyrrhiza uralensis/genetics/metabolism
*Stress, Physiological/genetics
*Plant Proteins/genetics/metabolism
*Computational Biology/methods
Phylogeny
*Transcription Factors/genetics/metabolism
Gene Expression Profiling
Droughts
*Multigene Family
Promoter Regions, Genetic
Transcriptome

@article {pmid41007943,
year = {2025},
author = {Zhu, Y and Zhao, Y and He, Y and Wu, B and Su, X},
title = {YOLO-WildASM: An Object Detection Algorithm for Protected Wildlife.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {18},
pages = {},
doi = {10.3390/ani15182699},
pmid = {41007943},
issn = {2076-2615},
support = {QNTD202308//Outstanding Youth Team Project of Central Universities/ ; 2023YFD2201700//National Key R&D Program of China/ ; },
abstract = {Wild animals are an essential component of natural ecosystems, and the accurate identification of wildlife targets plays a critical role in ecological conservation and species monitoring. However, the effectiveness of conventional object detection algorithms is often limited by the challenges posed by complex outdoor environments, small target sizes, and group occlusions. To address these issues, this study constructs a dataset comprising over 8000 images of 10 protected wildlife species and investigates effective detection methods for wildlife in natural habitats. We propose a novel deep learning-based detection framework, YOLO-WildASM, which incorporates three key improvements to the YOLOv8 architecture: a P2 detection layer for small objects, a multi-head self-attention (MHSA) mechanism, and a bidirectional feature pyramid network (BiFPN). Experimental results demonstrate that YOLO-WildASM significantly outperforms YOLOv8 and other state-of-the-art models on the custom wildlife dataset, achieving a mAP50 of 94.1%, which is 2.8% higher than the baseline model and superior to the latest YOLOv12 model (92.2%). Furthermore, ablation and generalization experiments validate the model's enhanced performance and adaptability in multi-scale wildlife detection tasks. The proposed deep learning-based detection framework provides an efficient and robust solution for wildlife monitoring and ecological conservation in complex natural ecosystems.},
}

@article {pmid41006295,
year = {2025},
author = {van Galen, LG and Smith, GR and Margenot, AJ and Waldrop, MP and Crowther, TW and Peay, KG and Jackson, RB and Yu, K and Abrahão, A and Ahmed, TA and Alatalo, JM and Anslan, S and Anthony, MA and Araujo, ASF and Ascher-Jenull, J and Bach, EM and Bahram, M and Baker, CCM and Baldrian, P and Bardgett, RD and Barrios-Garcia, MN and Bastida, F and Beggi, F and Benning, LG and Bragazza, L and Broadbent, AAD and Cano-Díaz, C and Cates, AM and Cerri, CEP and Cesarz, S and Chen, B and Classen, AT and Dahl, MB and Delgado-Baquerizo, M and Eisenhauer, N and Evgrafova, SY and Fanin, N and Fornasier, F and Francisco, R and Franco, ALC and Frey, SD and Fritze, H and García, C and García-Palacios, P and Gómez-Brandón, M and Gonzalez-Polo, M and Gozalo, B and Griffiths, R and Guerra, C and Hallama, M and Hiiesalu, I and Hossain, MZ and Hu, Y and Insam, H and Jassey, VEJ and Jiang, L and Kandeler, E and Kohout, P and Kõljalg, U and Krashevska, V and Li, X and Lu, JZ and Lu, X and Luo, S and Lutz, S and Mackie-Haas, KA and Maestre, FT and Malmivaara-Lämsä, M and Mangelsdorf, K and Manjarrez, M and Marhan, S and Martin, A and Mason, KE and Mayor, J and McCulley, RL and Moora, M and Morais, PV and Muñoz-Rojas, M and Murugan, R and Nottingham, AT and Ochoa, V and Ochoa-Hueso, R and Oja, J and Olsson, PA and Öpik, M and Ostle, N and Peltoniemi, K and Pennanen, T and Pescador, DS and Png, GK and Poll, C and Põlme, S and Potapov, AM and Priemé, A and Pritchard, W and Puissant, J and Rocha, SMB and Rosinger, C and Ruess, L and Sayer, EJ and Scheu, S and Sinsabaugh, RL and Slaughter, LC and Soudzilovskaia, NA and Sousa, JP and Stanish, L and Sugiyama, SI and Tedersoo, L and Trivedi, P and Vahter, T and Voriskova, J and Wagner, D and Wang, C and Wardle, DA and Whitaker, J and Yang, Y and Zhong, Z and Zhu, K and Ziolkowski, LA and Zobel, M and van den Hoogen, J},
title = {A global database of soil microbial phospholipid fatty acids and enzyme activities.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1568},
pmid = {41006295},
issn = {2052-4463},
support = {DEB-1845544//National Science Foundation (NSF)/ ; DEB-1926335//National Science Foundation (NSF)/ ; DGE 1450271//National Science Foundation (NSF)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; QUEX-CAS-QP-RD-18/19//Qatar Petroleum (QP)/ ; 305069/2018-7//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; I989-B16//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; CZ.02.01.01/00/22_008/0004635//Ministerstvo Školství, Mládeže a Tělovýchovy (Ministry of Education, Youth and Sports)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/I027037/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/N009452/1//RCUK | Natural Environment Research Council (NERC)/ ; PICT 2014-2838//Ministry of Science, Technology and Productive Innovation, Argentina | Agencia Nacional de Promoción Científica y Tecnológica (National Agency for Science and Technology, Argentina)/ ; 315260_149807//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; BIPD_01_2021_FCT-PTDC/BIA-CBI/2340/2020, UIDB/05937/2020, UIDP/05937/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; UID/EMS/00285/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816, Ei 862/29-1 and Ei 862/31-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG- FZT 118, 202548816//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 316045089//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 192626868-SFB 990//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 315415//Academy of Finland (Suomen Akatemia)/ ; PTDC/BIA-CBI/2340/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; ANR; MIXOPEAT; ANR-17-CE01-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 31872994//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41922056//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32101286//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32061143027//National Natural Science Foundation of China (National Science Foundation of China)/ ; CIDEGENT/2018/041//Generalitat Valenciana (Regional Government of Valencia)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; PRG1065, PRG1789, PSG784//Eesti Teadusagentuur (Estonian Research Council)/ ; NE/T012226//National Eye Research Centre (NERC)/ ; PRG1065, PRG1789, PSG784//Ministry of Education and Research | Estonian Research Competency Council (Research Competency Council)/ ; 2021M693360//China Postdoctoral Science Foundation/ ; },
mesh = {*Soil Microbiology ; *Phospholipids ; *Fatty Acids ; *Databases, Factual ; *Enzymes ; Soil/chemistry ; Ecosystem ; },
abstract = {Soil microbes drive ecosystem function and play a critical role in how ecosystems respond to global change. Research surrounding soil microbial communities has rapidly increased in recent decades, and substantial data relating to phospholipid fatty acids (PLFAs) and potential enzyme activity have been collected and analysed. However, studies have mostly been restricted to local and regional scales, and their accuracy and usefulness are limited by the extent of accessible data. Here we aim to improve data availability by collating a global database of soil PLFA and potential enzyme activity measurements from 12,258 georeferenced samples located across all continents, 5.1% of which have not previously been published. The database contains data relating to 113 PLFAs and 26 enzyme activities, and includes metadata such as sampling date, sample depth, and soil pH, total carbon, and total nitrogen. This database will help researchers in conducting both global- and local-scale studies to better understand soil microbial biomass and function.},
}

*Soil Microbiology
*Phospholipids
*Fatty Acids
*Databases, Factual
*Enzymes
Soil/chemistry
Ecosystem

@article {pmid41004955,
year = {2025},
author = {Qin, J and Wang, Q and Li, W},
title = {Incorporating regional green spaces into greenspace exposure assessment: A nationwide study of 244 Chinese cities.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127369},
doi = {10.1016/j.jenvman.2025.127369},
pmid = {41004955},
issn = {1095-8630},
abstract = {Green spaces are essential components of urban ecosystems, offering ecological services that support environmental sustainability and enhance human well-being. However, rapid urbanization has caused substantial declines in green space, particularly in rapidly growing cities. In this context, regional green spaces (RGSs), which are defined as green areas located beyond the boundaries of built-up areas, have gained attention for their ecological value and strategic role in enhancing urban resilience. Despite their importance, RGSs remain underrepresented in current greenspace exposure assessment frameworks. To fill this gap, we propose a novel transportation-weighted global greenspace exposure model that integrates RGSs, urban green spaces, and transportation proximity. Using greenspace exposure (GE) as an indicator, the model assesses the spatial distribution and exposure contribution of RGSs. We applied this model to 244 Chinese cities and obtained the following findings: (1) Incorporating RGSs significantly improves GE levels in many cities, particularly in southern and western regions, while also amplifying spatial disparities; (2) The compensatory effect of RGSs was validated, as substantial GE increases were observed under larger RGSs buffer zones; (3) Nighttime light intensity, elevation, and land surface temperature correlate strongly with GE, indicating the influence of both anthropogenic and natural factors. The proposed framework enhances the accuracy of GE assessments by integrating RGSs and transportation networks. Its scalable structure and moderate data requirements enable its application across diverse regions, supporting international efforts toward sustainable urban development.},
}

@article {pmid41003170,
year = {2025},
author = {Francesconi, L and Conti, M and Martellos, S and Di Nuzzo, L and Gheza, G and Nimis, PL and Pistocchi, C and Nascimbene, J},
title = {Dolichens: An Information System on the Lichens of the Dolomites.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {9},
pages = {},
doi = {10.3390/jof11090624},
pmid = {41003170},
issn = {2309-608X},
support = {DOT199RYN9-2//Ministero dell'università e della ricerca/ ; },
abstract = {Lichens, despite their key role as environmental indicators and their ecological importance, remain underrepresented in conservation policies, largely due to fragmented exploration of several areas, as well as limited availability of data in digital platforms. The UNESCO World Heritage area of the Dolomites (N Italy) is well-investigated as far as lichen diversity is concerned, with a long history of lichenological exploration since the 19th century. However, the relevant amount of data produced by these efforts was scattered and often not accessible in digital format, thus hindering data accessibility and usability. In this paper, we present Dolichens, a novel web platform designed to aggregate data about lichen diversity in the Dolomites. The platform aims at making available a comprehensive resource to support research, monitoring, and conservation of lichen diversity in the Dolomites, while ensuring data interoperability with the most relevant global repositories.},
}

@article {pmid41001881,
year = {2025},
author = {Rutz, A and Probst, D and Aguilar, C and Akiyama, DY and Alberti, F and Augustijn, HE and Avalon, NE and Beemelmanns, C and Barbieri, HB and Biermann, F and Bridge, AJ and Girón, EC and Cox, R and Crüsemann, M and D'Agostino, PM and Feuermann, M and Gerke, J and García, KG and Holme, JE and Hwang, JY and Iacovelli, R and Jeronimo Barbosa, JC and Kaur, N and Klapper, M and Köhler, AM and Korenskaia, A and Kubach, N and Lee, BT and Loureiro, C and Mantri, S and Narula, S and Meijer, D and Navarro-Muñoz, JC and Nguyen, GS and Paliyal, S and Panghal, M and Rao, L and Sieber, S and Sokolova, N and Sowa, ST and Szenei, J and Terlouw, BR and Weddeling, HG and Yu, J and Ziemert, N and Weber, T and Blin, K and van der Hooft, JJJ and Medema, MH and Zdouc, MM},
title = {MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf969},
pmid = {41001881},
issn = {1362-4962},
support = {21/07038-0//São Paulo Research Foundation/ ; 2021/08947-3//São Paulo Research Foundation/ ; 2023/06874-4//São Paulo Research Foundation/ ; MR/V022334/1//UKRI/ ; /AT/NCCIH NIH HHS/United States ; F32AT011475/GF/NIH HHS/United States ; 802736, MORPHEUS//Horizon 2020/ ; 101 000 392//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; 862 923//Horizon 2020/ ; 101 000 392//Horizon 2020/ ; 101 081 957//Horizon 2020/ ; 862 923//Horizon 2020/ ; //German Research Foundation/ ; 239748522//Deutsche Forschungsgemeinschaft/ ; 495740318//German Research Foundation/ ; //Hans-Fischer-Gesellschaft/ ; //State Secretariat for Education, Research and Innovation/ ; 102 022 750//SINTEF/ ; 102 029 187//SINTEF/ ; 102024676-14//SINTEF/ ; 102 029 407//SINTEF/ ; NNF23OC0086472//Novo Nordisk Foundation/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; //Department of Biotechnology/ ; //the Werner Siemens Foundation/ ; //DFG/ ; 101 072 485//Horizon Europe Marie Skłodowska-Curie/ ; //National Agri-Food and Biomanufacturing Institute (NABI)/ ; 948770-DECIPHER/ERC_/European Research Council/International ; 102 022 750//SINTEF/ ; 102 029 187//SINTEF/ ; 102024676-14//SINTEF/ ; 102 029 407//SINTEF/ ; //University Grants Commission/ ; //Horizon Europe programme/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; 101 072 485//Marie Skłodowska-Curie/ ; //German Center for Infection Research/ ; //Danish National Research Foundation/ ; //Horizon Europe programme/ ; //NWO/ ; //Horizon Europe programme/ ; KICH1.LWV04.21.013//Netherlands Organisation for Scientific Research/ ; },
abstract = {Secondary or specialized metabolites show extraordinary structural diversity and potent biological activities relevant for clinical and industrial applications. The biosynthesis of these metabolites usually starts with the assembly of a core 'scaffold', which is subsequently modified by tailoring enzymes to define the molecule's final structure and, in turn, its biological activity profile. Knowledge about reaction and substrate specificity of tailoring enzymes is essential for understanding and computationally predicting metabolite biosynthesis, but this information is usually scattered in the literature. Here, we present MITE, the Minimum Information about a Tailoring Enzyme database. MITE employs a comprehensive set of parameters to annotate tailoring enzymes, defining substrate and reaction specificity by the expressive reaction SMARTS (Simplified Molecular Input Line Entry System Arbitrary Target Specification) chemical pattern language. Both human and machine readable, MITE can be used as a knowledge base, for in silico biosynthesis, or to train machine-learning applications, and tightly integrates with existing resources. Designed as a community-driven and open resource, MITE employs a rolling release model of data curation and expert review. MITE is freely accessible at https://mite.bioinformatics.nl/.},
}

@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 {pmid41000208,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brown House-moth, Hofmannophila pseudospretella (Stainton, 1849).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {230},
pmid = {41000208},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hofmannophila pseudospretella (the Brown House-moth; Arthropoda; Insecta; Lepidoptera; Oecophoridae). The genome sequence is 406.2 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.5 kilobases in length.},
}

@article {pmid40998880,
year = {2025},
author = {Le Scornec, E and Chimienti, M and Corbeau, A and Pajot, A and Weimerskirch, H and Collet, J},
title = {Predicting fisheries from albatross movements requires accounting for individual variability in interaction.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32807},
pmid = {40998880},
issn = {2045-2322},
mesh = {Animals ; *Fisheries ; *Birds/physiology ; Geographic Information Systems ; *Animal Migration ; },
abstract = {Fisheries have major ecological impacts including bycatch of foraging seabirds, but it is often difficult to obtain comprehensive information on the presence of fishing vessels. Automatic Identification System (AIS) data can be used to monitor fisheries and their interactions with GPS-tracked seabirds, but not all vessels have their AIS operational. Bird-tied radar detectors can overcome this limit and complement monitoring, but the technology is recent and costly. We used both methods combined as a training dataset for classification algorithms, to extend the identification of interactions to GPS tracks without radar detectors nor AIS. We studied over 3 years wandering albatrosses from the French Southern Territories, interacting with toothfish and tuna longliners. We used 196 GPS tracks combined with radar detectors, to calculate different movement variables over various scales (time spent in an area, sinuosity, speed) and used a Random Forest to distinguish behaviour in presence or absence of fishing vessels. Our model reached high classification accuracy (ca. 85%) for individual birds included in the training dataset. However, we lost predictive power (around 72% of accuracy, with a drop of specificity from 76 to 59%) when predicting on individuals not included in the training dataset. Our results emphasize the importance of documenting and accounting for individual variations to use animals as sentinels. We discuss the pros and cons of different research avenues (data sampling, classification model, bird species, etc.) to eventually get to predict fisheries from bird movements only.},
}

Animals
*Fisheries
*Birds/physiology
Geographic Information Systems
*Animal Migration

@article {pmid40997692,
year = {2025},
author = {Zang, H and Feng, Y and Yang, F and Gao, S and Su, M and Li, H},
title = {Multi-media distribution, partitioning behavior, and environmental risk of per- and polyfluoroalkyl substances (PFASs) in the southern coastal zone of Shandong Peninsula, China.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107562},
doi = {10.1016/j.marenvres.2025.107562},
pmid = {40997692},
issn = {1879-0291},
abstract = {Per- and polyfluoroalkyl substances (PFASs) pose significant ecological threats due to their persistence and toxicity. This study investigates the occurrence, partitioning behavior, and environmental risks of 33 legacy and emerging PFASs in the southern coastal zone of Shandong Peninsula, China. Paired water and sediment samples were collected from 55 sites across groundwater, river, estuarine, tourist beaches and marine ranches. PFASs were ubiquitously detected, with total concentrations (∑PFASs) ranging from 23.41 to 80.62 ng/L in water and 0.38-6.49 ng/g dry weight (dw) in sediment. Except perfluorooctanoic acid (PFOA), perfluorobutanoic acid (PFBA) (6.42 ± 2.26 ng/L) and perfluorobutanesulfonic acid (PFBS) (3.03 ± 1.44 ng/L) dominated aqueous phases, reflecting phased-out replacements of long-chain homologs. Sediments accumulated long-chain compounds (e.g., Perfluorohexanoic acid (PFHxA): 0.92 ± 1.08 ng/g dw; perfluorooctane sulfonic acid (PFOS): 0.45 ± 0.28 ng/g dw), driven by hydrophobic partitioning. Strong positive correlations among long-chain PFASs (e.g., Perfluorododecanoic acid (PFDoDA)- perfluorotetradecanoic acid (PFTeDA), r = 0.882) indicated co-accumulation in organic-rich sediments. Spatial analysis revealed land-to-sea concentration gradients, with maxima in estuaries (52.72 ng/L) and industrial-adjacent sediments (6.48 ng/g dw). Groundwater infiltration (up to 51.53 ng/L) highlighted subsurface transport risks. Sediment-water partition coefficients (log Kd) increased with carbon chain length and salinity, consistent with salting-out effects and reduced electrostatic repulsion. Organic carbon-normalized log Koc values (Kow method) aligned with model predictions for most PFASs. Risk assessment identified high ecological risk for sediment-bound PFOS (RQ > 1) near river discharges, while PFOA posed greater aqueous-phase risks. Emerging PFASs (e.g., 6:2 chlorinated polyfluoroalkyl ether sulfonic acid (6:2 Cl-PFESA)) showed negligible risks. Coastal sediments act as significant PFASs reservoirs, with resuspension potential enabling secondary pollution.},
}

@article {pmid40996892,
year = {2025},
author = {Njoroge, SM and Kulohoma, BW and Falzon, LC and Kamanu, TK and Momanyi, K and Muinde, P and Murungi, MK and Ogendo, A and Ogola, J and Wambua, L and Kangethe, E and Rushton, J and Woolhouse, M and Thomson, NR and Kariuki, S and von Mentzer, A and Fèvre, EM},
title = {Genomic profiling of enterotoxigenic Escherichia coli toxins and adhesins in livestock isolates from Kenya.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001515},
pmid = {40996892},
issn = {2057-5858},
mesh = {*Enterotoxigenic Escherichia coli/genetics/isolation & purification/pathogenicity ; Kenya/epidemiology ; Animals ; *Livestock/microbiology ; *Escherichia coli Infections/microbiology/veterinary ; *Enterotoxins/genetics ; *Escherichia coli Proteins/genetics ; *Adhesins, Bacterial/genetics ; *Bacterial Toxins/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; Humans ; Feces/microbiology ; Cattle ; *Adhesins, Escherichia coli/genetics ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhoea in livestock and humans. The epidemiology of ETEC in animals remains understudied, prompting an investigation into the virulence factors and associated adhesins of ETEC in livestock from Western Kenya. Also, there is limited evidence supporting the role of livestock as possible zoonotic reservoirs for ETEC. ETEC strains harbour colonization factors/adhesins and enterotoxins, with animal ETECs exhibiting various adhesins (F4, F5, F6, F17, F18 and F41). Enterotoxins include heat-labile (LT) and heat-stable (ST) toxins and are further divided into LT-I and LT-II and STa and STb, respectively. Additional toxin combinations occur, with ETEC and Shiga toxin-producing E. coli (STEC) hybrids garnering public health significance. Here, we analysed faecal and mesenteric lymph node samples from diverse livestock across three Western Kenyan counties (Busia, Bungoma and Kakamega), using whole-genome sequencing. In silico screening determined the presence of AB5 and A2B5-like toxin genes, including cytolethal distending toxin (cdtABC) along with associated adhesins. To broaden the screening panel, adhesin genes identified were further characterized to identify both known and novel alleles, particularly focusing on human-ETEC colonization factors. Two estA alleles (estA-4-06, estA-6-02) and six eltAB-II toxin alleles (eltAB-II-a2-01, eltAB-II-a3-01, eltAB-II-c1-02, eltAB-II-c6-03, eltAB-II-c6-04 and eltAB-II-c7-02) were identified in livestock. Hybrid ETECs identified were ETEC/STEC present in 6.7% (4/60) of ETEC strains and ETEC with cdtABC type I. An A2B5-like tripartite toxin, potentially resembling the typhoid toxin, was detected in 8.7% (4/46) of the eltAB-II-positive strains. It may have unique effects on enterocytes distinct from known toxins. These findings expand our understanding of ETEC pathogenicity and genetic diversity in animal reservoirs, while also highlighting potential zoonotic risks. They broaden the toxin repertoire, offer adhesin-based vaccine candidates for livestock and provide valuable insights for future vaccine development and public health strategies in the Lake Victoria Crescent ecosystem and beyond.},
}

*Enterotoxigenic Escherichia coli/genetics/isolation & purification/pathogenicity
Kenya/epidemiology
Animals
*Livestock/microbiology
*Escherichia coli Infections/microbiology/veterinary
*Enterotoxins/genetics
*Escherichia coli Proteins/genetics
*Adhesins, Bacterial/genetics
*Bacterial Toxins/genetics
Virulence Factors/genetics
Whole Genome Sequencing
Humans
Feces/microbiology
Cattle
*Adhesins, Escherichia coli/genetics

@article {pmid40996715,
year = {2025},
author = {Fruggiero, I and Maisto, A and Passaro, S and Gentile, D and Nunziata, A and D'Agostino, N},
title = {A new database of chestnut DNA fingerprints for genetic diversity assessment, precise varietal identification, and traceability.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf056},
pmid = {40996715},
issn = {1758-0463},
support = {//Italy-Rural Development Programme/ ; //Italian Ministry of Agriculture/ ; },
mesh = {*Fagaceae/genetics ; *Genetic Variation ; Polymorphism, Single Nucleotide ; *DNA Fingerprinting ; *Databases, Genetic ; *DNA, Plant/genetics ; },
abstract = {The European chestnut (Castanea sativa Mill., Fagaceae) is ecologically and economically important, particularly in countries like Italy, Greece, Spain, and Turkey, where it supports rural economies and ecosystems. Accurate varietal recognition is crucial for managing chestnut groves but is hindered by the limitations of traditional methods, which require costly expertise and struggle to identify young, dormant, or scion trees. Recent advances in molecular tools, particularly single nucleotide polymorphism (SNP) markers identified through Kompetitive Allele-Specific PCR (KASP) technology, have transformed cultivar identification. To harness this potential, we developed KASTRACKdb, a genetic fingerprinting database for European chestnut that now integrates genotypic and phenotypic data for 150 chestnut accessions. Designed to translate KASP analysis results into practical and actionable insights, KASTRACKdb serves as a powerful tool for cultivar identification and management. The database offers three primary query modes and is designed for continuous upgrades, serving a crucial role in cataloguing the genetic diversity of chestnut trees, characterized by broad geographic distributions and significant genetic variation. This diversity is critical for conservation and breeding programs, enabling precise varietal identification and traceability to protect intellectual property, verify authenticity, and support the commercialization of high-value cultivars. Database URL: KASTRACKdb is available online at https://kastrack.crea.gov.it/kastrackdb/?lang=en.},
}

*Fagaceae/genetics
*Genetic Variation
Polymorphism, Single Nucleotide
*DNA Fingerprinting
*Databases, Genetic
*DNA, Plant/genetics

@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
doi = {10.1093/database/baaf060},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}

*Microbiota/genetics
Humans
*Databases, Genetic
Data Curation
Metadata
Animals
Metagenomics

@article {pmid40995615,
year = {2025},
author = {Kuhara, S and Matsugaki, R and Itoh, H and Oginosawa, Y and Fushimi, K and Matsuda, S and Saeki, S},
title = {Factors Influencing the Availability of Cardiopulmonary Exercise Testing for Patients Undergoing Cardiac Resynchronization Therapy in Japan.},
journal = {Journal of arrhythmia},
volume = {41},
number = {5},
pages = {e70198},
pmid = {40995615},
issn = {1880-4276},
abstract = {BACKGROUND: This study aimed to investigate the implementation rate of cardiopulmonary exercise testing (CPET) in patients undergoing cardiac resynchronization therapy (CRT) or cardiac resynchronization therapy-defibrillator (CRT-D), as well as the associated factors, using real-world data.

METHODS AND RESULTS: Data from the Diagnostic Procedure Combination System in Japan (2014-2018) was analyzed. The participants were cardiac patients who underwent CRT or CRT-D device implantation (n = 3859). The primary outcome was whether CPET was performed after device implantation. Unpaired t-tests and chi-squared tests were used to compare the characteristics of the CPET (+) and CPET (-) groups. Multivariate analysis was used to identify factors associated with CPET performance. CPET was performed in 134 patients (3%). The CPET (-) group was older and had lower Barthel Index (BI) scores at discharge. CPET (+) patients had a higher rate of cardiac rehabilitation. Multivariate analysis revealed that age < 70 years and BI score ≥ 85 at discharge were associated with CPET implementation. In-hospital cardiac rehabilitation is also an important determinant.

CONCLUSIONS: The CPET implementation after CRT or CRT-D was low. Emphasizing the importance of CPET may improve these rates. Future studies should explore strategies to increase its use in this patient population.},
}

@article {pmid40947031,
year = {2025},
author = {Onyeka, OC and Cheng, JS and Sanei, S and Clark, SL and Pinciotti, CM and Guzick, AG and Storch, EA and Stewart, S and Sandoval, JF and Taylor, L and Riddle, D and Garza, C and Liberzon, I and Rousseau, J and Shahidullah, JD and Newport, DJ and Wagner, KD and Nemeroff, C},
title = {Exploring resource profiles among trauma exposed youth: An identity-focused, cultural, and person-centered approach.},
journal = {Journal of affective disorders},
volume = {393},
number = {Pt A},
pages = {120298},
doi = {10.1016/j.jad.2025.120298},
pmid = {40947031},
issn = {1573-2517},
abstract = {OBJECTIVE: Resilience is a multi-faceted construct comprised of both internal and external resources that support adaptive functioning following trauma exposure. The role of resilience in ameliorating internalizing symptoms may depend on its typology as opposed to its presence alone, suggesting the existence of distinct subpopulations with heterogeneous resource profiles. The current study employs Latent Profile Analysis (LPA) to identify and characterize profiles of resilience-related resources among youth exposed to trauma from an identity-focused, cultural lens.

METHOD: Patterns of resources were examined in 1,538 youth (Mage = 13.4, 51.9% female) from a large longitudinal registry of trauma exposed youth in Texas using LPA. Profiles were related to demographic variables and internalizing symptoms (post-traumatic stress symptoms [PTSS], depression, and anxiety) using multinomial regression.

RESULTS: Results demonstrated an optimal four-class solution (Low Social Support and Average ERI, 31.2 %; Average Level of Protective Factors, 27.4 %; Ethnic Identity Diffusion, 18.1 %; Social Support Dominant, 23.2 %). Depressive symptoms significantly differentiated between classes in the four-class model as well as youth race, age, and ethnicity. Anxiety symptoms and PTSS did not differentiate the classes as clearly.

CONCLUSION: Person-centered analyses such as LPA underscore the value of examining resilience as a multi-faceted and heterogenous pattern of resources shaped by socio-ecological and cultural contexts among trauma-exposed youth. Implications for clinical intervention are discussed.},
}

@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 = {865694/ERC_/European Research Council/International ; 390713860//Deutsche Forschungsgemeinschaft/ ; RC2DK116713/DK/NIDDK NIH HHS/United States ; DP250103825//Australian Research Council/ ; 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 {pmid40571080,
year = {2025},
author = {Han, H and Zhang, JM and Li, K and Amankwah, JF and Zeng, XB and Shen, ZQ and Jin, XC and Chen, TY and Liu, JW and Liu, LP},
title = {Multi-omics and random forest reveal lipid metabolism disruption and biomarkers in grass carp (Ctenopharyngodon idellus) exposed to 2-methylisoborneol.},
journal = {Environmental research},
volume = {284},
number = {},
pages = {122226},
doi = {10.1016/j.envres.2025.122226},
pmid = {40571080},
issn = {1096-0953},
mesh = {Animals ; *Carps/metabolism ; *Lipid Metabolism/drug effects ; Biomarkers/metabolism ; *Water Pollutants, Chemical/toxicity ; *Camphanes/toxicity ; Liver/metabolism/drug effects ; Lipidomics ; Random Forest ; Multiomics ; },
abstract = {The lipophilic nature of 2-methylisoborneol (2-MIB), a prevalent off-flavor compound in aquatic systems, raises concerns about its bioaccumulation potential and metabolic interference in fish. Most studies have focused on removing this compound from water and fish. However, the effect of lipid metabolism in fish exposed to 2-MIB remains poorly defined. This study investigated lipid metabolism disruption in grass carp (Ctenopharyngodon idellus) induced by 96 h of exposure to 5 and 20 μg/L of 2-MIB through integrated serum biochemistry, hepatic lipidomics, and multi-omics analysis. Grass carp exhibited varying degrees of oxidative stress, immune response, and lipid metabolism disruption. Non-targeted lipidomic analysis reveals that 2-MIB alters the levels of phosphatidylcholine (PC), sphingomyelin (SM), and phosphatidylmethanol (PMeOH) in the liver, potentially affecting the structure and function of cell membranes. Multi-omics analysis suggests that pathways related to carbohydrate metabolism, lipid metabolism, and amino acid biosynthesis may be crucial in regulating the physiological status of grass carp. Additionally, random forest and correlation analysis identified pregnenolone and 1-cyano-2-methyl-2-propen-1-yl docosanoate as potential biomarkers for 2-MIB exposure. Collectively, this study highlights the lipid characteristics and mechanisms of grass carp under 2-MIB exposure, contributing to the evaluation of its impact on fish health and improving aquaculture management.},
}

Animals
*Carps/metabolism
*Lipid Metabolism/drug effects
Biomarkers/metabolism
*Water Pollutants, Chemical/toxicity
*Camphanes/toxicity
Liver/metabolism/drug effects
Lipidomics
Random Forest
Multiomics

@article {pmid38695096,
year = {2025},
author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T},
title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.},
journal = {Integrative zoology},
volume = {20},
number = {5},
pages = {916-935},
doi = {10.1111/1749-4877.12830},
pmid = {38695096},
issn = {1749-4877},
support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; China ; *Antelopes/microbiology/physiology ; Sheep/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; *Ruminants/microbiology/physiology ; *Adaptation, Physiological ; Parks, Recreational ; Bacteria/classification/genetics ; Feeding Behavior ; Multiomics ; },
abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.},
}

Animals
*Gastrointestinal Microbiome/physiology
China
*Antelopes/microbiology/physiology
Sheep/physiology/microbiology
RNA, Ribosomal, 16S/genetics
*Ruminants/microbiology/physiology
*Adaptation, Physiological
Parks, Recreational
Bacteria/classification/genetics
Feeding Behavior
Multiomics

@article {pmid40993501,
year = {2025},
author = {Garnier, É and Delalandre, L and Segrestin, J and Barkaoui, K and Kazakou, E and Navas, ML and Vile, D and Violle, C and Bernard-Verdier, M and Birouste, M and Blanchard, A and Bumb, I and Cruz, P and Debain, S and Fayolle, A and Fortunel, C and Grigulis, K and Laurent, G and Lavorel, S and Lloret, F and Pérez-Ramos, IM and Prieto, I and Roumet, C},
title = {FAIRTraits: An enriched, FAIR-compliant database of plant traits from Mediterranean populations of 240 species.},
journal = {Ecology},
volume = {106},
number = {9},
pages = {e70219},
doi = {10.1002/ecy.70219},
pmid = {40993501},
issn = {1939-9170},
support = {AAPFNSO2019OpenMetaPaper-14026//Ministère de l'Enseignement supérieur et de la Recherche (FNSO Project)/ ; },
abstract = {Trait-based ecology relies on high-quality, well-documented data to explore how plant traits relate to environmental conditions, community assembly, and ecosystem functioning. However, the reuse and synthesis of trait data across studies remain limited by several constraints: a lack of detailed metadata, heterogeneous protocols, absence of individual-level measurements, and underrepresentation of certain trait types-particularly below-ground traits. Many existing datasets also lack the environmental details necessary to investigate trait-environment relationships at local scales. Here, we present FAIRTraits, a comprehensive dataset that addresses these limitations by compiling 189,452 records of quantitative trait measurements collected between 1997 and 2023 from 1955 populations of 240 vascular plant species in the Northern Mediterranean Basin, a region known both for its exceptional biodiversity and as a climate change hotspot. All data were collected by a single research group using consistent and well-documented field and laboratory protocols, ensuring internal consistency across traits, species, sites, and years. FAIRTraits includes 180 traits measured at the individual or replicate level, with no aggregation. It features an unprecedented diversity of traits spanning all major plant organs-leaves, stems, roots, and reproductive parts. These include widely used traits such as specific leaf area and plant height, but also traits that are rarely reported, especially below-ground traits related to root morphology, as well as mechanical properties, phenology, and microbial associations. In addition to raw measurements, species are annotated with categorical descriptors (e.g., life form, photosynthetic pathway, and successional status), and species-level values taken from a Mediterranean flora, for key traits such as reproductive phenology and maximum height. To support analyses that account for environmental variability, each observation is linked to detailed descriptors of the plot where the individual was sampled, including climate data, soil physicochemical properties, and disturbance regime. Full metadata on sampling protocols and measurement methods are provided for every trait and environmental variable. FAIRTraits was built in compliance with the FAIR principles of data management (Findable, Accessible, Interoperable, and Reusable). Metadata are described using the Ecological Metadata Language (EML); trait definitions are standardized using community-endorsed semantic resources. The data are archived across two interoperable repositories: GBIF (via Darwin Core and trait-specific extensions) for taxon-trait associations and InDoRES for environmental and contextual data. These efforts ensure long-term preservation, data traceability, and seamless integration with plant trait databases such as BROT or TRY, and cross-organism initiatives such as the Open Traits Network or the Encyclopedia of Life. FAIRTraits offers a robust, richly documented, and reusable resource for investigating plant functional strategies, trait-environment relationships, and scaling from individuals to communities and ecosystems. It also provides a concrete example of how trait datasets can meet the highest standards of data quality and interoperability-serving as a model for future community-led initiatives in functional ecology. The FAIRTraits database is released under the CC-BY Attribution 4.0 International license.},
}

@article {pmid40991430,
year = {2025},
author = {Pascal, LV and Chadès, I and Adams, MP and Helmstedt, KJ},
title = {Developing new technologies to protect ecosystems: Planning with adaptive management.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {39},
pages = {e2422002122},
doi = {10.1073/pnas.2422002122},
pmid = {40991430},
issn = {1091-6490},
support = {DE200101791//Department of Education and Training | Australian Research Council (ARC)/ ; DE200100683//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {*Conservation of Natural Resources/methods ; *Ecosystem ; Climate Change ; Biodiversity ; Australia ; Coral Reefs ; },
abstract = {Technology development is an essential investment for policymakers to address contemporary global crises, including climate change, biodiversity loss, the energy transition, and emergent infectious diseases. However, investing limited resources in the development of new technologies is risky. The research and development process is unpredictable, with unknown timelines and outcomes. In addition, even after successful development, the effects of deploying a new technology remain uncertain. When confronted with these uncertainties, policymakers must determine how long they should allocate resources to developing new technologies. Informed decisions require anticipating possible successes and failures of both technology development and deployment, which is a challenging optimization task when managing dynamic systems, such as threatened ecological systems. Using an adaptive management approach from AI, we find a time limit new technologies should be developed for, which balances costs, benefits, and uncertainties during development and deployment. We extract clear and transparent general rules for investing in new technologies, building on an analytical approximation. Using Australia's Great Barrier Reef as a case study, we demonstrate that the development time limit ranges between 0 to 45 y before surrendering. We also show how characteristics of an ecological system influence the optimal investment strategy. Our approach can inform the development of new technologies in multiple domains including biodiversity conservation, public health, energy production, and the technology industry more broadly.},
}

*Conservation of Natural Resources/methods
*Ecosystem
Climate Change
Biodiversity
Australia
Coral Reefs

@article {pmid40920894,
year = {2025},
author = {Kawam, B and Ostner, J and McElreath, R and Schülke, O and Redhead, D},
title = {A causal framework for the drivers of animal social network structure.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013370},
doi = {10.1371/journal.pcbi.1013370},
pmid = {40920894},
issn = {1553-7358},
mesh = {Animals ; Bayes Theorem ; *Behavior, Animal/physiology ; Computational Biology ; *Social Behavior ; Computer Simulation ; Models, Biological ; },
abstract = {A major goal of behavioural ecology is to explain how phenotypic and ecological factors shape the networks of social relationships that animals form with one another. This inferential task is notoriously challenging. The social networks of interest are generally not observed, but must be approximated from behavioural samples. Moreover, these data are highly dependent: the observed network edges correlate with one another, due to biological and sampling processes. Failing to account for the resulting uncertainty and biases can lead to dysfunctional statistical procedures, and thus to incorrect results. Here, we argue that these problems should be understood-and addressed-as problems of causal inference. For this purpose, we introduce a Bayesian causal modelling framework that explicitly defines the links between the target interaction network, its causes, and the data. We illustrate the mechanics of our framework with simulation studies and an empirical example. First, we encode causal effects of individual-, dyad-, and group-level features on social interactions using Directed Acyclic Graphs and Structural Causal Models. These quantities are the objects of inquiry, our estimands. Second, we develop estimators for these effects-namely, Bayesian multilevel extensions of the Social Relations Model. Third, we recover the structural parameters of interest, map statistical estimates to the underlying causal structures, and compute causal estimates from the joint posterior distribution. Throughout the manuscript, we develop models layer by layer, thereby illustrating an iterative workflow for causal inference in social networks. We conclude by summarising this workflow as a set of seven steps, and provide practical recommendations.},
}

Animals
Bayes Theorem
*Behavior, Animal/physiology
Computational Biology
*Social Behavior
Computer Simulation
Models, Biological

@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 {pmid40053082,
year = {2025},
author = {Alibardi, L},
title = {Immunoreactivity of flexible and inflexible scales in different lizards indicates that the mature beta-layer contains different corneous proteins.},
journal = {Protoplasma},
volume = {262},
number = {5},
pages = {1129-1149},
pmid = {40053082},
issn = {1615-6102},
mesh = {Animals ; *Lizards/anatomy & histology/genetics/immunology/metabolism ; Immunohistochemistry ; *Animal Scales/cytology/immunology/metabolism ; *Reptilian Proteins/chemistry/genetics/immunology/metabolism ; Computational Biology ; Amino Acid Sequence ; Epitopes/immunology ; Peptides/chemistry/metabolism ; Keratins/chemistry/metabolism ; },
abstract = {We have analyzed by immunohistochemical methods the Oberhautchen-beta layer, here abbreviated as beta-layer, of lizards with hard scales and lizards with softer scales. Different antibodies for detecting Corneous Beta Proteins (CBPs) have been utilized. The agamid beta-corneous layer is generally 3-4 times thicker than in geckos, and the surface microornamentation forms a honeycomb pattern. Geckos feature thinner beta-layers and a spinulated pattern and show immunolocalization for CBPs and isopeptide bonds, a product of transglutaminase catalysis, in their thin beta-layer. CBPs and isopeptide-bonds are detected in the superficial Oberhautchen and alpha-layer of agamids while the beta-layer is immuno-negative. Considering the limitations of immunolabeling methods, the unexpected result might derive from inaccessibility of antibodies to epitopes that are masked within the packed corneous material of the agamid beta-layer. However, bioinformatics analysis for CBPs sequenced in the few species of agamids so far known indicates that these proteins have low identity with those of other lizards. This suggests that agamids possess peculiar CBPs but low isopeptide bonds in their inflexible beta-layer. In contrast, the thinner and pliable beta-corneous layers of geckos may derive from the presence of isopeptide bonds mixed with lower amounts of CBPs. The differences in material properties of lizard scales, inflexibility versus pliability, are adaptive for the different ecological conditions of the species here analyzed.},
}

Animals
*Lizards/anatomy & histology/genetics/immunology/metabolism
Immunohistochemistry
*Animal Scales/cytology/immunology/metabolism
*Reptilian Proteins/chemistry/genetics/immunology/metabolism
Computational Biology
Amino Acid Sequence
Epitopes/immunology
Peptides/chemistry/metabolism
Keratins/chemistry/metabolism

@article {pmid40986865,
year = {2025},
author = {Sun, Y and Jaiswal, A and Slade, C and Phillips, KT and Benzo, RM and Washington, P},
title = {Associations Between Social Determinants of Health and Adherence in Mobile-Based Ecological Momentary Assessment: Scoping Review.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e69831},
doi = {10.2196/69831},
pmid = {40986865},
issn = {1438-8871},
mesh = {Humans ; *Social Determinants of Health ; *Ecological Momentary Assessment ; *Patient Compliance ; Telemedicine ; Mobile Applications ; Male ; },
abstract = {BACKGROUND: Ecological momentary assessment (EMA) involves repeated prompts to capture real-time self-reported health outcomes and behaviors via mobile devices. With the rise of mobile health (mHealth) technologies, EMA has been applied across diverse populations and health domains. However, the extent to which EMA engagement and data quality vary across social determinants of health (SDoH) remains underexplored. Emerging evidence suggests that EMA adherence and data completeness may be sometimes associated with participant characteristics such as socioeconomic status, race/ethnicity, and education level. These associations may sometimes influence who engages with EMA protocols and the types of contextual data captured. Despite growing interest in these patterns, no review to date has synthesized evidence on how SDoH relate to EMA compliance and engagement.

OBJECTIVE: We conducted a scoping review to study two research questions: (R1) how EMA compliance rates in health studies can differ across SDoH and (R2) what types of SDoH have been identified through EMA health studies.

METHODS: Following PRISMA-ScR guidelines, we searched PubMed, Web of Science, and EBSCOhost using two sets of queries targeting EMA and its relationship to SDoH. Eligible studies were peer reviewed, were published in English between 2013 and 2024, and used mobile-based EMA methods. Studies were included if they (1) reported on differences in EMA compliance by SDoH or (2) reported at least one SDoH observed or uncovered during an EMA study. We used the social ecological model (SEM) as a guiding framework to categorize and interpret SDoH across individual, interpersonal, community, and societal levels. A qualitative thematic synthesis was conducted to iteratively and collaboratively extract, categorize, and review determinants.

RESULTS: We analyzed 48 eligible studies, of which 35 addressed R1 by examining compliance patterns across various SDoH. Using the SEM, we identified 13 determinants categorized across 4 levels: individual (eg, daily routine, biological sex, age, socioeconomic status, language, education, and race or ethnicity), interpersonal (eg, social support), community and organizational (eg, social context, social acceptance, stigmatization, and youth culture), and policy or societal (eg, systemic and structural barriers). These studies described differences in EMA response rates, compliance, and dropout associated with these determinants, often among vulnerable populations. The remaining 13 studies addressed R2, demonstrating examples of the types of SDoH that EMA research can uncover, including family culture, social support, social contexts, stigmatization, gender norms, heroic narratives, LGBTQ+ culture, racial discrimination, and systematic and structural barriers.

CONCLUSIONS: This scoping review illustrates how EMA compliance rates can differ across SDoH and highlights the potential of EMA to uncover social and cultural factors linked to health behaviors and outcomes. Our findings underscore the importance of integrating SDoH considerations into EMA study designs to capture context-specific sociocultural dynamics.},
}

Humans
*Social Determinants of Health
*Ecological Momentary Assessment
*Patient Compliance
Telemedicine
Mobile Applications
Male

@article {pmid40986480,
year = {2025},
author = {Constant, A and Paquin, V and Ackerman, RA and Depp, CA and Moore, RC and Harvey, PD and Pinkham, AE},
title = {Exploring the clinical utility of rhythmic digital markers for schizophrenia.},
journal = {PLOS digital health},
volume = {4},
number = {9},
pages = {e0001010},
doi = {10.1371/journal.pdig.0001010},
pmid = {40986480},
issn = {2767-3170},
abstract = {This study investigates the clinical utility of rhythmic digital markers (RDMs) in schizophrenia. RDMs are digital markers capturing behavioral rhythms over different timescales - within 24 hours span (ultradian), at a span of 24 hours (circadian), or over cycles of more than 24 hours (infradian). While previous research has explored digital markers for schizophrenia, the focus has primarily been on sensor data variability rather than rhythmic patterns. This study introduces two RDMs: an entropy RDM, which quantifies uncertainty in activity distribution over the infradian cycles, and a dynamic RDM, which is derived from models of transitions in entropy and psychotic symptom intensity using Markov chain analysis. Data were ecological momentary assessments (EMAs) of 39 activities collected from 390 individuals diagnosed with schizophrenia (N = 153) or bipolar disorder (N = 192) and controls (N = 45). We assessed associations between RDMs and symptom severity and whether participants could be differentiated based on these RDMs. We found that participants with schizophrenia significantly differed on dynamic RDMs, suggesting a potential diagnostic utility. However, dynamic RDMs were not associated with symptom severity, and entropy RDM had no significant clinical correlate. Our findings contribute to the growing evidence on digital markers in psychiatry and highlight the potential of rhythmic digital markers (RDMs) in characterizing digital phenotypes for schizophrenia.},
}

@article {pmid40481658,
year = {2025},
author = {von Mering, S and Leachman, S and Santos, J and Meudt, HM},
title = {Wikidata for botanists: benefits of collaborating and sharing Linked Open Data.},
journal = {Annals of botany},
volume = {136},
number = {3},
pages = {491-511},
doi = {10.1093/aob/mcaf062},
pmid = {40481658},
issn = {1095-8290},
support = {//Fundação para a Ciência e Tecnologia/ ; },
mesh = {*Botany ; *Information Dissemination/methods ; *Internet ; Knowledge Bases ; *Databases, Factual ; },
abstract = {BACKGROUND: Wikidata is a multilingual linked open knowledge base to which anyone can contribute that contains multitudes of botany-related information. Wikidata reveals interactions between entities and connects botany-related information from multiple institutions and other sources, benefiting the botanical community in numerous ways. The aim of this article is to give an overview of Wikidata from a botany perspective and issue a call to action to the botanical community to collectively improve the quantity and quality of information related to botany, botanists and botanical collections, in Wikidata. Here, we use a broad definition of botany to include the study of many different taxa and specializations.

SCOPE: Wikidata contains botany-related data and identifiers for botanists and botanical collectors, botanical taxa, natural history institutions and collections, botany-related publications, geographical locations and research expeditions, as well as genes, genetic variants, chemical compounds, diseases, and more. As an open, collaborative and community-curated knowledge base, Wikidata enables different communities to add and link data related to botany and empowers the querying and reuse of this data via digital tools such as the Wikidata Query Service, Bionomia, Scholia, TL-2 and Expeditia.

CONCLUSIONS: Collaboration is key in botany and Wikidata, and the sharing and enriching of botany-related Linked Open Data benefits us all. Several resources, including ethical and legal guidelines, are available for botanists to edit, use, reuse, roundtrip and teach Wikidata. We call on all botanists to be active participants in Wikidata, improving the quality, quantity and linking of botany-related data. Our individual and collective actions can help harness the power of Linked Open Data to answer important queries in the field, improve accessibility of herbaria, increase visibility of botanists and their scientific contributions, integrate Wikidata into the classroom, support the Madrid Declaration strategic actions, achieve our collective goals, and ultimately make botany-related information more FAIR (Findable, Accessible, Interoperable, Reusable) and equitable.},
}

*Botany
*Information Dissemination/methods
*Internet
Knowledge Bases
*Databases, Factual

@article {pmid40296452,
year = {2025},
author = {Wang, S and Kaur, S and Kunath, BJ and May, P and Richardson, L and Rogers, AB and Wilmes, P and Finn, RD and Vizcaíno, JA},
title = {An Approach to Integrate Metagenomics, Metatranscriptomics and Metaproteomics Data in Public Data Resources.},
journal = {Proteomics},
volume = {25},
number = {17-18},
pages = {33-42},
doi = {10.1002/pmic.202500002},
pmid = {40296452},
issn = {1615-9861},
support = {C19/BM/13684739//National Research Fund Luxembourg (FNR)/ ; 223745/Z/21/Z//Wellcome/ ; //EMBL Core Funding/ ; },
mesh = {*Metagenomics/methods ; *Proteomics/methods ; Humans ; Databases, Protein ; Metagenome ; *Transcriptome ; Animals ; Pilot Projects ; },
abstract = {The availability of public metaproteomics, metagenomics and metatranscriptomics data in public resources such as MGnify (for metagenomics/metatranscriptomics) and the PRIDE database (for metaproteomics), continues to increase. When these omics techniques are applied to the same samples, their integration offers new opportunities to understand the structure (metagenome) and functional expression (metatranscriptome and metaproteome) of the microbiome. Here, we describe a pilot study aimed at integrating public multi-meta-omics datasets from studies based on human gut and marine hatchery samples. Reference search databases (search DBs) were built using assembled metagenomic (and metatranscriptomic, where available) sequence data followed by de novo gene calling, using both data from the same sampling event and from independent samples. The resulting protein sets were evaluated for their utility in metaproteomics analysis. In agreement with previous studies, the highest number of peptide identifications was generally obtained when using search DBs created from the same samples. Data integration of the multi-omics results was performed in MGnify. For that purpose, the MGnify website was extended to enable the visualisation of the resulting peptide/protein information from three reanalysed metaproteomics datasets. A workflow (https://github.com/PRIDE-reanalysis/MetaPUF) has been developed allowing researchers to perform equivalent data integration, using paired multi-omics datasets. This is the first time that a data integration approach for multi-omics datasets has been implemented from public data available in the world-leading MGnify and PRIDE resources.},
}

*Metagenomics/methods
*Proteomics/methods
Humans
Databases, Protein
Metagenome
*Transcriptome
Animals
Pilot Projects

@article {pmid40979437,
year = {2025},
author = {Atagong, SD and Tonnang, H and Senagi, K and Wamalwa, M and Agboka, KM and Odindi, J},
title = {A review on knowledge and information extraction from PDF documents and storage approaches.},
journal = {Frontiers in artificial intelligence},
volume = {8},
number = {},
pages = {1466092},
pmid = {40979437},
issn = {2624-8212},
abstract = {INTRODUCTION: Automating the extraction of information from Portable Document Format (PDF) documents represents a major advancement in information extraction, with applications in various domains such as healthcare, law, or biochemistry. However, existing solutions face challenges related to accuracy, domain adaptability, and implementation complexity.

METHODS: A systematic review of the literature was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology to examine approaches and trends in PDF information extraction and storage approaches.

RESULTS: The review revealed three dominant methodological categories: rule-based systems, statistical learning models, and neural network-based approaches. Key limitations include the rigidity of rule-based methods, the lack of annotated domain-specific datasets for learning-based approaches, and issues such as hallucinations in large language models.

DISCUSSION: To overcome these limitations, a conceptual framework is proposed comprising nine core components: project manager, document manager, document pre-processor, ontology manager, information extractor, annotation engine, question-answering tool, knowledge visualizer, and data exporter. This framework aims to improve the accuracy, adaptability, and usability of PDF information extraction systems.},
}

@article {pmid40963762,
year = {2025},
author = {Dey, D and Lateef, HA and Leroux, A and Zipunnikov, V and Merikangas, K},
title = {Associations Between Daily Outdoor Temperature and Subjective Real-time Ratings of Emotional States and Sleep in Mood Disorder Subtypes.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40963762},
abstract = {Growing evidence for the influence of weather on mental health at both the aggregate level indices of mental health statistics of hospitalizations, morbidity, and mortality, and individual level dynamics of mood states. Most research on this topic has focused on light exposure and depressed mood as the sole indicators of seasonal fluctuations of mood disorders. This paper evaluates the association between daily maximum outdoor temperature (DMOT) and contemporaneously reported mood, energy, anxiousness, and sleep quality assessed with Ecological Momentary Assessment (EMA) in a community-based sample of 452 people, aged 11 to 85 years, comprising people with or without a history of mood disorders. After controlling for demographics, daily activity levels, and daytime cloud coverage as an index of light exposure, we found that higher DMOT was associated with better mood, increased energy, and better sleep quality among those with with a history of mood disorders, particularly in the spring among people with a history of Bipolar Disorder (BD) who tended to exhibit more seasonal changes than controls. These findings suggest that the dynamics of mood, energy, and sleep may underlie the aggregate population-level influences of temperature and correlated environmental influences on negative mental health outcomes, particularly among those with BD. Therefore, the conceptualization of risk and intervention for mood disorders should consider both the aggregate influences of temperature and light and associated environmental conditions, as well as individual-level sleep quality and energy as potential mechanisms for seasonal patterns of emotional states.},
}

@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 {pmid40980745,
year = {2024},
author = {Boyes, D and Broad, GR and Sivess, L and Holt, S and Holland, PWH and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown China-mark moth, Elophila nymphaeata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {155},
pmid = {40980745},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Elophila nymphaeata (the Brown China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 734.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,079 protein coding genes.},
}

@article {pmid40976215,
year = {2025},
author = {Kakuma, M and Wada, T and Murakami, M and Tatsuno, T and Ishii, N and Kobayashi, NI and Kurosawa, T and Sayama, Y and Nihei, N and Ohte, N},
title = {Environmental and biological drivers of [137]Cs accumulation in freshwater fish across forested and downstream sites in Fukushima.},
journal = {Journal of environmental radioactivity},
volume = {290},
number = {},
pages = {107810},
doi = {10.1016/j.jenvrad.2025.107810},
pmid = {40976215},
issn = {1879-1700},
abstract = {To elucidate ecological factors governing [137]Cs accumulation in freshwater fish, we examined 10 species collected from forested headwater streams and downstream reaches of rivers flowing through the Fukushima evacuation zone between 2020 and 2022. By integrating land cover data with isotopic and body size metrics, our study clarifies mechanisms shaping radiocesium distribution across fish communities in post-accident environments. Individuals exceeding the Japanese regulatory limit of 100 Bq/kg-wet were found at all sites, and fish/water concentration ratios of [137]Cs varied widely, from 9.7 × 10 L/kg-wet in a sea-run masu salmon to 1.2 × 10[6] L/kg-wet in a Japanese dace. White-spotted charr and masu salmon, both typical stream-dwelling salmonids, exhibited significantly higher concentration ratios than the other species. Fish from areas with greater forest cover exhibited consistently elevated [137]Cs concentrations, indicating that forests serve as persistent sources of radiocesium to aquatic food webs more than a decade after the accident. Stable isotope analysis showed a significant positive association between terrestrial carbon contribution and [137]Cs concentration, demonstrating that individuals assimilating more terrestrial-derived resources tended to accumulate higher contamination. A positive relationship was also observed between relative body size and [137]Cs concentration, suggesting that growth-related traits influence accumulation. These results suggest that forest connectivity, dietary reliance on allochthonous resources, and individual growth characteristics collectively influence the accumulation of [137]Cs in freshwater fish. The approach and findings provide quantitative evidence for species- and site-specific processes underlying long-term radiocesium dynamics in forested river networks, informing risk assessment and fisheries management in radiologically impacted landscapes.},
}

@article {pmid40972996,
year = {2025},
author = {Paladan, S and Kumbar, B and Govindasamy, D and Patil, S and Chethan Kumar, HB and Yogisharadhya, R and Yadav, P and Vivian, TJW and Gaekwad, SS and Kumar, N and Gulati, BR and Shivachandra, SB and Chanda, MM},
title = {Unravelling ecological factors influencing phylodynamics of Kyasanur Forest Disease in India.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105831},
doi = {10.1016/j.meegid.2025.105831},
pmid = {40972996},
issn = {1567-7257},
abstract = {Kyasanur Forest Disease Virus (KFDV) is a tick-borne flavivirus endemic to the Western Ghats region of India, with increasing reports of geographic expansion. This study employs phylogenetic analysis and spatial diffusion modeling to understand the evolutionary dynamics and transmission patterns of KFDV. Whole genome and E-gene sequences were analysed to identify major phylogenetic clusters, transmission velocity, and environmental factors influencing viral spread. The analysis revealed two primary phylogenetic clusters: Cluster A, originating in Karnataka, and linked to initial outbreaks (1957-1972) and subsequent re-emergence post-2010 in Karnataka, Kerala, and Goa; and Cluster B, which expanded from Maharashtra in the late 1970s into Tamil Nadu, Karnataka, and Kerala. Phylogenetic findings indicated a slow mutation rate, indicative of long-term viral persistence in sylvatic reservoirs rather than sustained human transmission. Spatial diffusion analysis estimated a median transmission velocity of 59.67 km/year. Environmental factors such as deforestation, land cover change, and livestock density acted as facilitators of viral spread, while urbanization, open water bodies, and precipitation served as resistance factors. The findings underscore the need for enhanced surveillance, ecological monitoring, and public health interventions to mitigate the increasing risk of KFD outbreaks. This study provides a comprehensive framework for understanding KFDV transmission and evolution, integrating phylogenetic and ecological data to improve risk assessment and guide control strategies in both endemic and emerging regions.},
}

@article {pmid40971902,
year = {2025},
author = {Gontjes, KJ and Singh, A and Sansom, SE and Boyko, JD and Smith, SA and Lautenbach, E and Snitkin, E},
title = {Phylogenetic context of antibiotic resistance provides insights into the dynamics of resistance emergence and spread.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf478},
pmid = {40971902},
issn = {1537-6613},
abstract = {BACKGROUND: To ameliorate the antibiotic resistance crisis, the drivers of resistance emergence and resistance spread must be better understood.

METHODS: Whole-genome sequencing and susceptibility testing were performed on clinical carbapenem-resistant Klebsiella pneumoniae isolates collected from August 2014 to July 2015 across 12 long-term acute care hospitals. Ancestral state reconstruction partitioned patients with resistant strains into those that likely acquired resistance via de novo evolution or cross-transmission. Logistic regression was used to evaluate the associations between patient characteristics/exposures and these two pathways: resistance due to predicted within-host emergence of resistance, and resistance due to predicted cross-transmission. This framework is available in the user-friendly R package, phyloAMR (https://github.com/kylegontjes/phyloAMR).

RESULTS: Phylogenetic analysis of 386 epidemic lineage carbapenem-resistant Klebsiella pneumoniae sequence type 258 isolates revealed differences in the relative contribution of de novo evolution and cross-transmission to the burden of resistance to five antibiotics. Clade-specific variations in rates of resistance emergence and their frequency and magnitude of spread were detected for each antibiotic. Phylogenetically-informed regression modeling identified distinct clinical risk factors associated with each pathway. Exposure to the cognate antibiotic was an independent risk factor for resistance emergence (trimethoprim-sulfamethoxazole, colistin, and novel beta-lactam/beta-lactamase inhibitors) and resistance spread (trimethoprim-sulfamethoxazole, amikacin, and colistin). In addition to antibiotic exposures, comorbidities (e.g., stage IV+ decubitus ulcers) and indwelling medical devices (e.g., gastrostomy tubes) were detected as unique risk factors for resistance spread.

CONCLUSIONS: Phylogenetic contextualization generated insights and hypotheses into how bacterial genetic background, patient characteristics, and clinical practices influence the emergence and spread of antibiotic resistance.},
}

@article {pmid40971328,
year = {2025},
author = {Bock, O and Huang, JY and Wigge, M and Bieche, C and Kehm, C and Richter, N and Fink, GR and Onur, OA},
title = {Route-following deficits in amnestic mild cognitive impairment: Is the dual encoding of route-following strategies impaired?.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251378658},
doi = {10.1177/13872877251378658},
pmid = {40971328},
issn = {1875-8908},
abstract = {BackgroundOne of the earliest signs of amnestic mild cognitive impairment (MCI) and neurodegenerative dementia (ND) is spatial disorientation, e.g., getting lost on previously familiar routes. Healthy individuals often follow routes by combining two strategies, serial recall of directions and cue-direction associations, but the integration of these two strategies may be degraded in amnestic MCI and ND.ObjectiveTo evaluate whether impaired integration of the two strategies (dual encoding) contributes to the route-following deficits in amnestic MCI.MethodsTwenty-five patients with amnestic MCI and 25 age-matched healthy controls (HC) followed routes through virtual mazes that allowed the use of the serial order strategy only (maze S), the associative cue strategy only (maze A), or both strategies (maze SA).ResultsFor longer routes, accuracy in maze SA exceeded that in mazes S and A, confirming the existence of a dual encoding benefit. The magnitude of this benefit was comparable in both groups. In contrast, performance on an additional dual-task test was poorer in MCI than in HC.ConclusionsWe attribute the dissociation between preserved dual encoding and impaired dual-tasking in amnestic MCI not to fundamental differences in the underlying mechanisms, but rather to the different ecological validity of the two experimental paradigms. Our findings suggest that spatial orientation training in amnestic MCI need not target dual encoding.},
}

@article {pmid40489655,
year = {2025},
author = {Kruse, PM and Ring, CL},
title = {A cheminformatics workflow for higher-throughput modeling of chemical exposures from biosolids.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {207},
number = {1},
pages = {126-138},
doi = {10.1093/toxsci/kfaf081},
pmid = {40489655},
issn = {1096-0929},
support = {/EPA/EPA/United States ; //Oak Ridge Institute for Science and Education/ ; //Department of Energy/ ; /EPA/EPA/United States ; DE-SC0014664//Oak Ridge Associated Universities/ ; //Center for Computational Toxicology and Exposure/ ; //Office of Research and Development/ ; /EPA/EPA/United States ; },
mesh = {Workflow ; Humans ; *Sewage/chemistry ; *Cheminformatics/methods ; United States Environmental Protection Agency ; *High-Throughput Screening Assays ; United States ; *Environmental Exposure ; Risk Assessment ; Software ; },
abstract = {The U.S. Environmental Protection Agency's Biosolids Screening Tool can predict potential human and ecological exposures to chemical contaminants in treated sewage sludge biosolids, but large quantities of chemical-specific physico-chemical data are required to parameterize the model. Here, an R workflow is presented that leverages publicly available databases of chemical information, particularly the U.S. EPA's CompTox Chemicals Dashboard, to prepare data for model simulations using the Biosolids Screening Tool. The workflow is publicly available at https://github.com/USEPA/CompTox-ExpoCast-autoBST. The automated Biosolids Screening Tool workflow (autoBST) reduces the time to gather data necessary to screen hundreds of chemicals from days to just a few minutes. autoBST is a practical example of the utility of leveraging the US EPA CompTox Chemicals Dashboard. autoBST provides transparent and reproducible data retrieval and input into existing models, allowing assessors to defensibly prioritize chemicals in biosolids that may pose a risk to human health or the environment.},
}

Workflow
Humans
*Sewage/chemistry
*Cheminformatics/methods
United States Environmental Protection Agency
*High-Throughput Screening Assays
United States
*Environmental Exposure
Risk Assessment
Software

@article {pmid40970218,
year = {2024},
author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B},
title = {Establishing the ELIXIR Microbiome Community.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {},
doi = {10.12688/f1000research.144515.2},
pmid = {40970218},
issn = {2046-1402},
mesh = {*Microbiota ; *Metagenomics/methods ; Computational Biology ; },
abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.},
}

*Microbiota
*Metagenomics/methods
Computational Biology

@article {pmid40968609,
year = {2025},
author = {Kim, EM and Koh, DH and Sung, S and Hong, Y and Moon, S and Lee, JE and Ko, KP and Park, SK and Min, J and Choi, S and Park, JH and Lee, SG and Kim, HC and Park, DU and Kim, I},
title = {Fraction of Cancer Attributable to Occupational Carcinogens in Korea between 2015 and 2030.},
journal = {Cancer research and treatment},
volume = {},
number = {},
pages = {},
doi = {10.4143/crt.2025.193},
pmid = {40968609},
issn = {2005-9256},
abstract = {PURPOSE: To estimate the contribution of occupational carcinogens to cancer incidence and mortality in the Korean population between 2015 and 2030.

MATERIALS AND METHODS: We selected occupational carcinogens classified as International Agency for Research on Cancer (IARC) Group 1 and estimated the prevalence of exposure using data from the Korean CARcinogen EXposure (K-CAREX) and previous studies. Relative risks were calculated using published literature through a meta-analysis. Levin's formula was used to estimate population attributable fraction (PAF) while considering a 15-year latency period between exposure, cancer incidence, and death. Additionally, trends in cancer PAF were calculated up to 2030, assuming constant relative risks and a 15-year latency period.

RESULTS: In 2015, the PAFs for occupational carcinogen-related cancer incidence and mortality were 1.00% (men: 1.75%, women: 0.15%) and 1.97% (men: 2.97%, women: 0.33%), respectively, with asbestos being the largest contributor (incidence: 0.48%; mortality: 0.98%). In 2030, the PAFs for occupational carcinogen-related cancer incidence and mortality were 0.34% (men: 0.62%, women: 0.07%) and 0.80% (men: 1.22%; women: 0.15%), respectively, with diesel engine exhaust being projected to become the largest contributor by 2030 (incidence: 0.16%, mortality: 0.41%).

CONCLUSION: The PAFs of occupational carcinogens in Korea between 2015 and 2030 were estimated to be very low in the general population, and the values are expected to decrease over time owing to various regulations to prevent exposure to occupational carcinogens. Therefore, while regulating well-known occupational carcinogens, efforts should be made to monitor newly identified ones to ensure prompt implementation of preventive measures.},
}

@article {pmid40966233,
year = {2025},
author = {Lee, J and Suh, Y},
title = {Physical activity and its associated factors among adults with chronic kidney disease in a community setting: A secondary data analysis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0332604},
doi = {10.1371/journal.pone.0332604},
pmid = {40966233},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Renal Insufficiency, Chronic/physiopathology/epidemiology ; *Exercise/physiology ; Middle Aged ; Adult ; Aged ; Republic of Korea/epidemiology ; Nutrition Surveys ; Glomerular Filtration Rate ; Quality of Life ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Physical activity in patients with chronic kidney disease is important as it helps lowers blood pressure, reduces inflammatory markers, improves cognitive function, and improves health-related quality of life. However, there is a lack of studies accurately assess physical activity levels in this population.

OBJECTIVE: This study aimed to examine the characteristics of chronic kidney disease patients across eGFR stages, assess the proportion of Korean adults with chronic kidney disease meeting recommended physical activity levels, and identify the factors associated with meeting the weekly physical activity recommendation.

METHODS: We conducted a secondary analysis of data from the 2016-2020 Korean National Health and Nutrition Examination Survey. Descriptive statistics and logistic regression were used to examine physical activity patterns and associated factors.

RESULTS: Among CKD patients, 79.5% engaged in insufficient physical activity. Factors significantly associated with sufficient activity included sex, smoking status, activity limitation, and eGFR.

CONCLUSIONS: Tailoring physical activity interventions is crucial, considering the patient's clinical condition, physical performance, and demographic factors.},
}

Humans
Male
Female
*Renal Insufficiency, Chronic/physiopathology/epidemiology
*Exercise/physiology
Middle Aged
Adult
Aged
Republic of Korea/epidemiology
Nutrition Surveys
Glomerular Filtration Rate
Quality of Life
Secondary Data Analysis

@article {pmid40965697,
year = {2025},
author = {Serpico, J and Choi, KH and Zambrano-Luna, BA and Wang, TX and Wang, H},
title = {Decoding the spatial spread of cyanobacterial blooms in an epilimnion.},
journal = {Journal of mathematical biology},
volume = {91},
number = {4},
pages = {44},
pmid = {40965697},
issn = {1432-1416},
support = {Individual Discovery Grant RGPIN-2020-03911//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Accelerator Supplement Award RGPAS-2020-00090//Natural Sciences and Engineering Research Council of Canada/ ; Tier 1 Canada Research Chair Award//Canada Research Chairs/ ; },
mesh = {*Cyanobacteria/growth & development ; *Lakes/microbiology ; *Models, Biological ; Ecosystem ; Biomass ; Mathematical Concepts ; Geographic Information Systems ; *Eutrophication ; Computer Simulation ; Environmental Monitoring/statistics & numerical data ; *Harmful Algal Bloom ; },
abstract = {Cyanobacterial blooms (CBs) pose significant global challenges due to their harmful toxins and socio-economic impacts, with nutrient availability playing a key role in their growth, as described by ecological stoichiometry (ES). However, real-world ecosystems exhibit spatial heterogeneity, limiting the applicability of simpler, spatially uniform models. To address this, we develop a spatially explicit partial differential equation model based on ES to study cyanobacteria in the epilimnion of freshwater systems. We establish the well-posedness of the model and perform a stability analysis, showing that it admits two linearly stable steady states, leading to either extinction or a spatially uniform positive equilibrium where cyanobacterial biomass stabilizes at its carrying capacity. Further, we discuss the possibility of long-term spatially nonuniform solution with small diffusion and space-dependent parameters. We use the finite elements method (FEM) to numerically solve our system on a real lake domain derived from Geographic Information System (GIS) data and realistic wind conditions extrapolated from ERA5-Land. Additionally, we use a cyanobacteria estimation (CE) obtained from Sentinel-2 to set initial conditions, and we achieve strong model validation metrics. Our numerical results highlight the importance of lake shape and size in bloom monitoring, while global sensitivity analysis using Sobol Indices identifies light attenuation and intensity as primary drivers of bloom variation, with water movement influencing early bloom stages and nutrient input becoming critical over time. This model supports continuous water-quality monitoring, informing agricultural, recreational, economic, and public health strategies for mitigating CBs.},
}

*Cyanobacteria/growth & development
*Lakes/microbiology
*Models, Biological
Ecosystem
Biomass
Mathematical Concepts
Geographic Information Systems
*Eutrophication
Computer Simulation
Environmental Monitoring/statistics & numerical data
*Harmful Algal Bloom

@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 {pmid40962773,
year = {2025},
author = {Zhao, ZL and Jiang, X and Su, Y and Yin, LJ and Luo, T and Zhao, WQ and Luo, JH},
title = {[Analysis of Vegetation Changes and Influencing Factors in Guiyang City over the Past 33 Years Based on the kNDVI and OPGD Model].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {9},
pages = {5839-5849},
doi = {10.13227/j.hjkx.202408129},
pmid = {40962773},
issn = {0250-3301},
mesh = {China ; *Ecosystem ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; Cities ; *Models, Theoretical ; *Conservation of Natural Resources ; *Plant Development ; Geographic Information Systems ; Satellite Imagery ; },
abstract = {The vegetation index is a critical indicator for monitoring changes in terrestrial ecosystems， and understanding the spatiotemporal characteristics of vegetation changes and their potential driving factors is essential for improving regional ecological protection and management. This study utilized eight periods of Landsat remote sensing images from 1990 to 2023 to calculate the kernel normalized difference vegetation index （kNDVI） for Guiyang City using the Google Earth engine （GEE） platform. The Theil-Sen + Mann-Kendall trend analysis method was applied to assess the trends and significance levels of kNDVI changes， and the Hurst index was used to evaluate the persistence and future trends of kNDVI. Additionally， the optimal parameters geographic detector （OPGD） was employed to analyze the driving mechanisms behind the spatial differentiation of kNDVI. The study produced the following results： ① From 1990 to 2023， the kNDVI in Guiyang City exhibited a fluctuating upward trend over four distinct phases， with significant spatial differentiation， generally displaying a north-high， south-low distribution pattern. ② Over the 33 years， 74.62% of the area in Guiyang City experienced improvement in vegetation cover， while 25.14% showed signs of degradation. ③ The average Hurst index was 0.610 2， indicating weak persistence and suggesting a trend of continued improvement into the future for vegetation kNDVI in Guiyang City. ④ The land-use type factor （0.231 2） showed the strongest explanatory power for the spatial differentiation of vegetation kNDVI. The interactions between factors exhibited both nonlinear enhancement and bi-factor enhancement， with the combination of land use and other factors synergistically explaining the spatial differentiation of kNDVI more effectively.},
}

China
*Ecosystem
*Environmental Monitoring/methods
*Remote Sensing Technology
Cities
*Models, Theoretical
*Conservation of Natural Resources
*Plant Development
Geographic Information Systems
Satellite Imagery

@article {pmid40959203,
year = {2025},
author = {Beene, D and Lin, Y and Hoover, JH and Shi, X},
title = {Deconstructing rurality to better "place" health data.},
journal = {International journal of geographical information science : IJGIS},
volume = {},
number = {},
pages = {},
pmid = {40959203},
issn = {1365-8816},
abstract = {Rural-urban classification schemes are frequently used in ecological studies of population health. However, the algorithms used to produce these classifications as well as their underlying assumptions may not match their intended use in health research. Here, we focus on the spatial distribution of features of the physical environment that are related to health - such as healthcare - to examine the extent to which eight classification schemes capture the heterogeneous context of rural places. We further explore how well rural-urban classifications distinguish between different types of rural places by comparing rural Tribal reservations with other rural areas in the American southwest. Because health services and infrastructure are often distributed through state and federal programs to underserved populations in rural areas, this approach speaks to the broader political implications in how rural communities are defined and represented. Results indicate that rural-urban classifications do not adequately reflect heterogeneous contexts within and across rural places. We advocate for more appropriate population health models that explain contextual differences in the relationship between health and place.},
}

@article {pmid40958166,
year = {2025},
author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG},
title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70178},
doi = {10.1111/1462-2920.70178},
pmid = {40958166},
issn = {1462-2920},
support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; },
abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.},
}

*Metagenome
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism
Soil Microbiology
Phylogeny
*Microbiota/genetics
Computational Biology/methods
*Bacterial Proteins/genetics/chemistry
*Databases, Protein
Protein Conformation

@article {pmid40726282,
year = {2025},
author = {de Mol, F and Fritzsche, R and Gerowitt, B},
title = {Weed biodiversity and herbicide intensity as linked via a decision support system.},
journal = {Pest management science},
volume = {81},
number = {10},
pages = {6667-6677},
doi = {10.1002/ps.70019},
pmid = {40726282},
issn = {1526-4998},
support = {//South Baltic Cross-border cooperation EU programme/ ; //German Federal Agency/ ; FKZ 351984070//Federal Ministry/ ; },
mesh = {*Herbicides ; *Biodiversity ; *Plant Weeds/drug effects ; *Weed Control/methods ; Germany ; *Decision Support Techniques ; Triticum/growth & development ; },
abstract = {BACKGROUND: Extensive herbicide use is one reason for the declining biodiversity of arable weeds. This study aimed to investigate (i) whether herbicide decisions recommended by a decision support system increase the weed species diversity compared to standard recommendations, and (ii) whether high weed species diversity reduces herbicide intensity, which in turn contributes to higher diversity. Data on weeds and herbicide applications in winter wheat fields in north-eastern Germany were collected in 15 field trials over 2 years. Five treatments differed in the way of decision-making for herbicide application, including two treatments according to recommendations of decision support systems.

RESULTS: Along the Hill's series biodiversity metrics, the untreated control had the highest species richness (13.5 m[-2]) per field but showed increasingly stronger dominance structures than the treated plots (equivalent species richness: 1.7-2.0 m[-2]). The treatment frequency index as a metric for herbicide intensity was significantly lowest in the decision support system with low reliability (1.07). Path models, including weed diversity and density in autumn, weed diversity in summer, and herbicide intensity as a mediating variable showed a significant decreasing effect of Shannon diversity on herbicide intensity in all treatments. Only the decision support systems reacted to low weed densities with a significant reduction of the herbicide intensity.

CONCLUSION: Higher weed species diversity contributes to lower herbicide intensity, which is ecologically and economically valuable. Decision support systems for herbicide application should have other target functions than cost reduction for contributing to biodiversity. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

*Herbicides
*Biodiversity
*Plant Weeds/drug effects
*Weed Control/methods
Germany
*Decision Support Techniques
Triticum/growth & development

@article {pmid40643351,
year = {2025},
author = {Wang, ZR and Yu, H and Yang, ZL},
title = {Cystinarius: phylogeny and species diversity in China.},
journal = {Mycologia},
volume = {117},
number = {5},
pages = {983-999},
doi = {10.1080/00275514.2025.2518029},
pmid = {40643351},
issn = {1557-2536},
mesh = {China ; *Phylogeny ; *Agaricales/cytology/genetics ; Databases, Genetic ; },
abstract = {Cystinarius is a small genus belonging to the family Cortinariaceae, distinguished by its distinctive combination of small basidiospores and presence of both cheilo- and pleurocystidia, a combination that is rarely found in other genera within the Cortinariaceae. To date, this genus consists of only two subgenera and includes seven recognized species. Previously, only a single specimen of Cy. crassus was reported from China. Based on the analysis of 17 newly collected specimens, supported by morphological evidence and two-locus phylogenetic inference, five species, namely, Cy. fulvellus, Cy. longipes, Cy. shennongensis, Cy. crassus, and Cy. paurigarhwalensis, were recognized. Among them, the former three species are new to science, whereas the last one is new to China. This study provides comprehensive taxonomic descriptions and a detailed identification key to the Cystinarius species discovered in China.},
}

China
*Phylogeny
*Agaricales/cytology/genetics
Databases, Genetic

@article {pmid40957742,
year = {2025},
author = {Seven, OF and Bicer, M and Adli, MA},
title = {Experimental insights into muscle and joint roles in stumble recovery: A scoping review.},
journal = {Gait & posture},
volume = {},
number = {},
pages = {109963},
doi = {10.1016/j.gaitpost.2025.08.081},
pmid = {40957742},
issn = {1879-2219},
abstract = {INTRODUCTION: A major concern, often resulting in serious injuries and loss of independence, is caused by falls due to stumbling. Previous works, investigating stumble recovery responses isolated to joint or muscle responses, lacks a comprehensive view of coordinated whole-body recovery.

METHODS: A scoping review, on Web of Science, Scopus and PubMed, was conducted using keywords related to recovery from anteriorly-directed stumbles induced by physical obstruction of the swing limb during healthy human walking. Extracted data were experimental cohort, swing phase during stumble, perturbation apparatus, recovery strategies, biomechanical responses including joint kinematics, kinetics and muscle activity. A narrative synthesis was provided to summarize findings across studies.

RESULTS: 23 of 337 identified studies met inclusion criteria. Limited focus on older adults or comparing them to young adults were found. Rigid and stationary obstacles were commonly used, while compliant/movable obstacles were rarely examined, limiting ecological validity. Recovery strategies varied by perturbation timing: foot elevation and lowering in early/mid-swing and late swing stumbles, respectively. Rare responses like delayed lowering and reaching were underexplored. Sagittal plane lower-limb kinematics were frequently reported, with often missing trunk motion, joint moments and EMG from proximal muscles.

CONCLUSION: This review highlights the importance of rapid and coordinated whole-body responses in stumble recovery, particularly involving the support limb and trunk. Findings suggest rehabilitation should target hip extensor strength, trunk control and support limb engagement to improve recovery. Future research should investigate underexplored strategies, trunk and upper-limb involvement and age-related adaptations to enhance intervention design.},
}

@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; Animals ; Humans ; *Homeostasis ; RNA, Ribosomal, 16S/genetics ; Aged ; Metabolomics/methods ; Metagenomics ; *Trichuriasis/parasitology/microbiology ; *Trichuris ; Female ; Male ; Bacteria/classification/genetics/isolation & purification ; Metabolic Networks and Pathways ; Aged, 80 and over ; Metabolome ; *Intestines/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}

*Gastrointestinal Microbiome
Animals
Humans
*Homeostasis
RNA, Ribosomal, 16S/genetics
Aged
Metabolomics/methods
Metagenomics
*Trichuriasis/parasitology/microbiology
*Trichuris
Female
Male
Bacteria/classification/genetics/isolation & purification
Metabolic Networks and Pathways
Aged, 80 and over
Metabolome
*Intestines/microbiology
Multiomics

@article {pmid40936754,
year = {2025},
author = {Ward, EJ and English, PA and Rooper, CN and Ferriss, BE and Whitmire, CE and Wetzel, CR and Barnett, LAK and Anderson, SC and Thorson, JT and Johnson, KF and Indivero, J and Markowitz, EH},
title = {surveyjoin: a standardized database of scientific trawl surveys in the Northeast Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19964},
pmid = {40936754},
issn = {2167-8359},
mesh = {Pacific Ocean ; *Fisheries/statistics & numerical data ; *Databases, Factual/standards ; Animals ; Gadiformes ; Biomass ; Surveys and Questionnaires ; Conservation of Natural Resources ; },
abstract = {Fisheries management faces challenges due to political, spatial, and ecological complexities, which are further exacerbated by variation or shifts in species distributions. Effective management depends on the ability to integrate fisheries data across political and geographic boundaries. However, such efforts may be hindered by inconsistent data formats, limited data sharing, methodological differences in sampling, and regional governance differences. To address these issues, we introduce the surveyjoin R package, which combines and provides public access to bottom trawl survey data collected in the Northeast Pacific Ocean by NOAA Fisheries and Fisheries and Oceans Canada. This initial database integrates over 3.3 million observations from 14 bottom trawl surveys spanning Alaska, British Columbia, Washington, Oregon, and California from the 1980s to present. This database standardizes variables such as catch-per-unit-effort (CPUE), haul data, and in-situ measurements of bottom temperature. We demonstrate the utility of this database through three case studies. Our first case study develops a coastwide biomass index for Pacific hake (Merluccius productus) using geostatistical index standardization, comparing results to independent acoustic survey estimates. The second case study examines spatial patterns in groundfish community structure, highlighting breakpoints between assemblages in their mixture of life histories and trophic compositions. Our third example applies spatially varying coefficient models to assess sablefish (Anoplopoma fimbria) biomass trends, identifying regional variability in increases in occurrence and biomass. Together, these case studies demonstrate how the surveyjoin R package and database may improve species and ecosystem assessments by providing insights into population trends across geopolitical boundaries. This database and package represent an important step toward offering a scalable framework that can be extended to include additional data types, surveys, and species. By fostering collaboration, transparency, and data-driven decision making, surveyjoin supports international efforts to sustainably manage shared marine resources under dynamic environmental conditions.},
}

Pacific Ocean
*Fisheries/statistics & numerical data
*Databases, Factual/standards
Animals
Gadiformes
Biomass
Surveys and Questionnaires
Conservation of Natural Resources

@article {pmid40920814,
year = {2025},
author = {Bergman, DR and Jackson, T and Jain, HV and Norton, KA},
title = {An efficient and flexible framework for inferring global sensitivity of agent-based model parameters.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013427},
pmid = {40920814},
issn = {1553-7358},
mesh = {*Models, Biological ; Humans ; Computational Biology/methods ; Computer Simulation ; Cell Proliferation/physiology ; Algorithms ; Neoplasms/pathology ; Reproducibility of Results ; },
abstract = {Agent-based models (ABMs) have become essential tools for simulating complex biological, ecological, and social systems where emergent behaviors arise from the interactions among individual agents. Quantifying uncertainty through global sensitivity analysis is crucial for assessing the robustness and reliability of ABM predictions. However, most global sensitivity methods demand substantial computational resources, making them impractical for highly complex models. Here, we introduce SMoRe GloS (Surrogate Modeling for Recapitulating Global Sensitivity), a novel, computationally efficient method for performing global sensitivity analysis of ABMs. By leveraging explicitly formulated surrogate models, SMoRe GloS allows for comprehensive parameter space exploration and uncertainty quantification without sacrificing accuracy. We demonstrate our method's flexibility by applying it to two biological ABMs: a simple 2D in vitro cell proliferation model and a complex 3D vascular tumor growth model. Our results show that SMoRe GloS is compatible with simpler methods like the Morris one-at-a-time method, and more computationally intensive variance-based methods like eFAST. SMoRe GloS accurately recovered global sensitivity indices in each case while achieving substantial speedups, completing analyses in minutes. In contrast, direct implementation of eFAST amounted to several days of CPU time for the complex ABM. Remarkably, our method also estimates sensitivities for ABM parameters representing processes not explicitly included in the surrogate model, further enhancing its utility. By making global sensitivity analysis feasible for computationally expensive models, SMoRe GloS opens up new opportunities for uncertainty quantification in complex systems, allowing for more in depth exploration of model behavior, thereby increasing confidence in model predictions.},
}

*Models, Biological
Humans
Computational Biology/methods
Computer Simulation
Cell Proliferation/physiology
Algorithms
Neoplasms/pathology
Reproducibility of Results

@article {pmid40954274,
year = {2025},
author = {Moore, TR and Krobath, DM and Chang Chusan, YA and Sanga, U and Webb, P and Pachucki, M and Cuevas, A and Roland, HB and Grant, B and Economos, CD and Nicholson, V and Kumanyika, S},
title = {Systems science methods reveal and address links between discrimination and health disparities in US food systems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {40954274},
issn = {2662-1355},
support = {K99HD109456//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
}

@article {pmid40950394,
year = {2025},
author = {Sambo, B and Sperotto, A and Aznarez, C and Terzi, S and Pittore, M and Critto, A and Torresan, S},
title = {Managing the water-energy-food nexus in the adige river basin: impacts of climate and land use change on ecosystem services bundles.},
journal = {Climatic change},
volume = {178},
number = {9},
pages = {168},
pmid = {40950394},
issn = {0165-0009},
abstract = {UNLABELLED: The Water-Energy-Food (WEF) nexus framework highlights the interdependencies among water, energy, and food systems. Integrating Ecosystem Services (ESs) enhances this approach by incorporating ecological benefits for more holistic assessments. This study applies a spatially explicit ESs-based WEF nexus analysis in the Adige River Basin (Northern Italy), focusing on five ESs: water provisioning, crop yield, sediment retention, carbon storage, and landscape diversity, under two future scenarios (SSP1-RCP 2.6 and SSP5-RCP 8.5) from 2018 to 2050. Using Self-Organizing Maps, sub-basins were clustered into ESs bundles enabling the identification of tailored management strategies. Results reveal spatial heterogeneity and shifts in ESs bundles, with synergies often found in upstream, forested areas. Under high-emission scenarios, regulating services decline and provisioning services face trade-offs, especially with intensified agriculture. Key strategies suggested include maintaining environmental flows, reducing synthetic fertilizers, promoting reforestation, crop diversification, and expanding protected areas. These are structured into physical, economic, and climatic pathways aligned with EU restoration goals. Findings demonstrate the value of an ESs-bundles approach for optimizing synergies and managing trade-offs across the WEF nexus.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10584-025-04013-3.},
}

@article {pmid40938934,
year = {2025},
author = {Attar, MI and Naseer, S and Pandey, Y and Khan, JN and Bangroo, SA and Hasan, MA and Khan, ZA and Khan, AH and Tantray, AM},
title = {Morphometric analysis for prioritizing critical areas of Urpash watershed in Sindh catchment of the lesser Himalayas using RS and GIS approach.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330503},
pmid = {40938934},
issn = {1932-6203},
mesh = {*Geographic Information Systems ; *Rivers ; *Remote Sensing Technology ; Hydrology ; Conservation of Natural Resources ; Environmental Monitoring/methods ; Soil Erosion ; Himalayas ; },
abstract = {Effective soil and water conservation is critical in fragile watersheds prone to erosion. However, assessing erosion susceptibility in ungauged watersheds remains challenging due to the lack of observed hydrological data This study addresses this gap by employing a comprehensive morphometric analysis integrated with remote sensing (RS) and Geographic Information Systems (GIS) to prioritize erosion-prone sub-watersheds within the ecologically sensitive and data-scarce Urpash watershed. Shuttle Radar Topography Mission (SRTM) Digital Elevation Model (DEM) data and ArcGIS 10.7 were used to analyze a 21.37 km[2] area. Key morphometric parameters-including linear, areal, and relief aspects-were assessed to understand watershed hydrology and erosion susceptibility. A total of 32 streams were identified, categorized into 1st to 3rd orders. Watershed shape indices, such as elongation ratio (Re = 0.65), form factor (Rf = 0.33) and circularity ratio (Rc = 0.295), indicate an elongated shape, indicative of reduced surface runoff and erosion potential, along with higher sub-soil permeability. However, drainage parameters like drainage density (Dd = 1.67 km/km2), stream frequency (Fs = 1.49 km-2) and drainage intensity (Di = 0.89 km-1) pointed to the watershed's susceptibility to flooding, gully erosion, and landslides due to slow surface runoff dispersion. Relief parameters such as basin relief (H = 1742.87 m), relief ratio (Rh = 0.22) and ruggedness number (Rn = 2.9) reflect the watershed's high relief and steep terrain, indicating a greater susceptibility to erosion. Using a compound parameter approach, the sub-watershed prioritisation ranked WS3 as the highest priority, followed by WS4, WS5, WS6, WS2, and WS1. By using RS and GIS-based morphometric analysis in an ungauged Urpash watershed, this study provides a geospatial framework for targeted soil and water conservation strategies, contributing to more precise watershed management in data-scarce and erosion-vulnerable regions.},
}

*Geographic Information Systems
*Rivers
*Remote Sensing Technology
Hydrology
Conservation of Natural Resources
Environmental Monitoring/methods
Soil Erosion
Himalayas

@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 {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 {pmid40941648,
year = {2025},
author = {Pantelić, M and Cvetković, D and Jovankić, J and Soldatović, I and Pantelić, M and Dujović, M and Vučinić, T and Cvetković, A},
title = {Predictive Value of Serum HMGB1, NF-κB, and IL-17 Gene Expression in Acute Pancreatitis Outcomes.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172160},
pmid = {40941648},
issn = {2075-4418},
abstract = {Background/Objectives: This study investigated the gene expression levels of High Mobility Group Box 1 (HMGB1), nuclear factor kappa B (NF-κB) and interleukin-17 (IL-17) in the serum of patients with acute pancreatitis (AP) and analyzed the correlation of these three with the severity of AP, local and systemic complications, transfer to intensive care unit (ICU) and death. Methods: AP was diagnosed and stratified according to the revised Atlanta classification. The diagnosis of AP requires two of the following three features: abdominal pain (acute onset of persistent severe, epigastric pain often radiating to the back); serum lipase/or amylase activity at least three times higher than normal; characteristic findings of AP on computed tomography or abdominal ultrasonography. Results: This study confirmed that NF-kB is a significant marker of AP severity, as well as for ICU transfer, and correlates with acute respiratory distress syndrome (ARDS), while IL-17 is shown as a significant marker of systemic complications (pleural effusions, ARDS, and renal failure). HMGB1 correlates with pancreatic necrosis, systemic inflammatory response syndrome, and ICU transfer. Conclusions: Over the past years, the role of HMGB1, NF-kB, and IL-17 in the pathogenesis of AP has been under intense scrutiny, and they have been proposed as prognostic biomarkers for AP severity, poor prognosis, and death outcome. The advantage of this research is that changes in gene expression can be detected before the increase in serum concentrations of these biomarkers, and it allows early prediction of a severe form of AP, as well as the development of complications.},
}

@article {pmid40934430,
year = {2025},
author = {Tejada-Llacsa, PJ and Alarcón, GS and Ugarte-Gil, MF},
title = {Prevalence of systemic lupus erythematosus in Peru and its association with environmental and healthcare factors: An ecological study.},
journal = {Lupus},
volume = {},
number = {},
pages = {9612033251379313},
doi = {10.1177/09612033251379313},
pmid = {40934430},
issn = {1477-0962},
abstract = {ObjectiveTo estimate the prevalence of Systemic Lupus Erythematosus (SLE) in Peru in 2017 and its association with altitude, environmental temperature, and physician density.MethodsThis ecological study was performed using population data from the 2017 Peruvian census. The number of SLE cases for each department was obtained from the National Health Registries using the ICD-10 code M32. Altitude, environmental temperature and physician density were obtained for each department from the National Institute of Statistics and Informatic (Instituto Nacional de Estadística e Informática) registries. The prevalence for each department was calculated adjusting for age and sex. Then a negative binomial regression was performed to estimate the prevalence ratio (PR) and evaluate factors associated with the prevalence of SLE.ResultsThe national prevalence of SLE was 40.2 per 100,000 people. Two age groups had the highest prevalence: 12-17 years and 30-59 years. Females exhibited a higher prevalence than males, particularly in the 30-59 age group (113.9 vs 16.1 per 100,000, respectively). An inverse relationship was observed between the age- and sex-adjusted prevalence in each department and altitude (PR 0.97; 95% CI: 0.94-0.99). On the other hand, there was a direct relationship with physician density (PR: 1.04; 95% CI: 1.01-1.07). No association was found between the adjusted prevalence and environmental temperature or latitude.ConclusionThe prevalence of SLE in Peru aligns with global estimates. The inverse relationship with altitude and the direct association with physician density suggest that environmental and healthcare access factors may influence disease distribution. Further research is needed to explore the underlying mechanisms driving these associations.},
}

@article {pmid40932046,
year = {2025},
author = {Matsumoto, Y and Okada, G and Ohta, M},
title = {Can Augmented Reality be Used as a Portion Size Estimation Aid Tool? A Pilot Randomized Controlled Trial.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {38},
number = {5},
pages = {e70125},
doi = {10.1111/jhn.70125},
pmid = {40932046},
issn = {1365-277X},
support = {//This study was supported by PUH Research Grant Program./ ; },
mesh = {Humans ; Pilot Projects ; *Portion Size/psychology ; Female ; Male ; Young Adult ; Adult ; *Augmented Reality ; *Dietetics/education/methods ; Students ; Feasibility Studies ; },
abstract = {BACKGROUND: Evidence on the effectiveness of augmented reality (AR)-based tools for portion size estimation as an educational aid remains limited. In this pilot study, we developed a 3D food model using AR and assessed the feasibility of using this application to teach portion size estimation skills.

METHODS: This intervention study involved 43 students (including 38 females) from two dietetic education institutions. Participants were randomly assigned into four groups: (1) text only, (2) text and pictures, (3) food model and (4) AR. Learning effectiveness was evaluated using a pretest of 10 different foods, followed by a 10-min instructional session with the assigned tool, and then a post-test. Participants rated each learning tool for enjoyment, usefulness and recommendation to others on an 11-point Likert scale. Outcomes included the change in the number of correct answers within ± 10% or ± 20% of the true food weight.

RESULTS: Mean acceptability ratings for the text only, text and picture, food model and AR groups were enjoyment (4.1, 5.6, 7.0 and 7.9), usefulness (5.5, 7.4, 8.4 and 8.3) and recommendation to others (3.6, 6.3, 6.3 and 7.1), respectively. The mean changes in correct answers for text only, text and picture, food model and AR groups were 0.7, -1.1, 1.5 and 0.1, respectively, within a 10% error margin, and 1.2, -1.9, 2.0 and 0.8, respectively, within a 20% error margin.

CONCLUSIONS: This pilot study suggests that AR-based tools have potential as educational aids for portion size estimation among future dietitians, with acceptability ratings comparable to conventional methods, such as text only, text and pictures, and food models.

TRIAL REGISTRATION: The study was registered with the University Hospital Medical Information Network; UMIN000054307.},
}

Humans
Pilot Projects
*Portion Size/psychology
Female
Male
Young Adult
Adult
*Augmented Reality
*Dietetics/education/methods
Students
Feasibility Studies

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40930298,
year = {2025},
author = {Slack, SD and Esquinca, E and Arehart, CH and Boorgula, MP and Szczesny, B and Romero, A and Campbell, M and Chavan, S and Rafaels, N and Watson, H and Landis, RC and Hansel, NN and Rotimi, CN and Olopade, CO and Figueiredo, CA and Ober, C and Liu, AH and Kenny, EE and Kammers, K and Ruczinski, I and Taub, MA and Daya, M and Gignoux, CR and Kechris, K and Barnes, KC and Mathias, RA and Johnson, RK},
title = {Prediction and Characterization of Genetically-Regulated Expression of Asthma Tissues from African-Ancestry Populations.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.07.035},
pmid = {40930298},
issn = {1097-6825},
abstract = {BACKGROUND: Genetic control of gene expression in asthma-related tissues is not well-characterized, particularly for African-ancestry populations, limiting advancement in our understanding of the increased prevalence and severity of asthma in those populations.

OBJECTIVE: To create novel transcriptome prediction models for asthma tissues (nasal epithelium and CD4+ T cells) and apply them in transcriptome-wide association study to discover candidate asthma genes.

METHODS: We developed and validated gene expression prediction databases for unstimulated CD4+ T cells and nasal epithelium using an elastic net framework. Combining these with existing prediction databases (N=51), we performed TWAS of 9,284 individuals of African-ancestry to identify tissue-specific and cross-tissue candidate genes for asthma.

RESULTS: Novel databases for CD4+ T cells and nasal epithelial gene expression prediction contain 8,351 and 10,296 genes, respectively, including four asthma loci (SCGB1A1, MUC5AC, ZNF366, LTC4S) not predictable with existing public databases. Prediction performance was comparable to existing databases and was most accurate for populations sharing ancestry with the training set (e.g. African ancestry). From transcriptome-wide association study, we identified 17 candidate causal asthma genes (adjusted P<0.1), including genes with tissue-specific (IL33 in nasal epithelium) and cross-tissue (CCNC and FBXW7) effects.

CONCLUSIONS: Expression of IL33, CCNC, and FBXW7 may affect asthma risk in African ancestry populations by mediating inflammatory responses. The addition of CD4+ T cell and nasal epithelium prediction databases to the public sphere will improve ancestry representation and power to detect novel gene-trait associations from transcriptome-wide association study.},
}

@article {pmid40928529,
year = {2025},
author = {Lawler, T and Kwekkeboom, K and Warren Andersen, S and Sethi, AK and Tevaarwerk, AJ and Litzelman, K and Pophali, PA and Gangnon, RE and Hampton, JM and LoConte, NK and Trentham-Dietz, A},
title = {Self-efficacy for cancer self-management in the context of COVID-19: a cross-sectional survey study.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {33},
number = {10},
pages = {843},
pmid = {40928529},
issn = {1433-7339},
support = {UL1TR002373//National Institutes of Health, United States/ ; P30CA014520/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Self Efficacy ; *COVID-19/epidemiology/psychology ; Middle Aged ; Male ; Female ; Cross-Sectional Studies ; Adult ; Aged ; *Neoplasms/therapy/psychology ; *Self-Management/psychology ; Adolescent ; *Cancer Survivors/psychology ; Aged, 80 and over ; Young Adult ; Surveys and Questionnaires ; },
abstract = {PURPOSE: For cancer survivors, self-efficacy is needed to manage the disease and the effects of treatment. The COVID-19 pandemic disrupted cancer-related healthcare, which may have impacted self-management self-efficacy. We investigated self-efficacy reported by cancer survivors during COVID-19, including associations with healthcare disruptions, distress, and general health.

METHODS: Between 2020 and 2021, 1902 individuals aged 18-80 years with a recent cancer diagnosis completed a survey regarding the effects of COVID-19 on healthcare, self-efficacy for managing cancer and social interactions, cancer-related distress, and perceived general health. Linear and logistic models estimated odds ratios and 95% confidence intervals (CIs) between self-efficacy scores, healthcare disruptions, significant distress, and general health.

RESULTS: Mean self-efficacy for managing cancer was 7.58 out of 10. Greater self-efficacy was associated with lower odds for distress (OR 0.18 [95% CI 0.13-0.26], quartile 4 vs. 1) and for worse general health (0.05 [0.03-0.09]). Participants with disruptions to cancer-related healthcare had lower self-efficacy for managing cancer compared to those without (6.62 vs. 7.09, respectively, P < 0.001) and higher odds for distress (1.70 [1.36-2.14]), but not worse general health (1.13 [0.39-1.44]). Lower self-efficacy mediated 27% of the association between healthcare disruptions and increased distress (15-47%). Associations with self-efficacy for managing social interactions trended in the same direction.

CONCLUSIONS: During COVID-19, disruptions to cancer-related healthcare were associated with lower self-efficacy, increased distress, and worse general health. Psychosocial interventions designed to overcome barriers and target self-efficacy may be important for enhancing outcomes among cancer survivors experiencing disruptions in healthcare access.},
}

Humans
*Self Efficacy
*COVID-19/epidemiology/psychology
Middle Aged
Male
Female
Cross-Sectional Studies
Adult
Aged
*Neoplasms/therapy/psychology
*Self-Management/psychology
Adolescent
*Cancer Survivors/psychology
Aged, 80 and over
Young Adult
Surveys and Questionnaires

@article {pmid40927873,
year = {2025},
author = {Blackman Carr, LT and Ard, J and Shanks, CB and Forman, EM and Goldstein, SP and Haire-Joshu, D and Jastreboff, AM and Johnson, S and Kandula, NR and Katzmarzyk, PT and Keyserling, TC and Kumanyika, SK and Lee, BY and Lewis, KH and Martin, MY and Mozaffarian, D and Newton, RL and Odoms-Young, A and Panza, E and Pronk, NP and Rosas, LG and Samuel-Hodge, C and Schmidt, LA and Sherwood, NE and Spring, B and Cooksey Stowers, K and Baskin, ML},
title = {Toward Health Equity: A Workshop Report on the State of the Science of Obesity Interventions for Adults.},
journal = {Obesity (Silver Spring, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/oby.70035},
pmid = {40927873},
issn = {1930-739X},
support = {/HL/NHLBI NIH HHS/United States ; //Office of Disease Prevention/ ; /NH/NIH HHS/United States ; },
abstract = {OBJECTIVE: From October 18-20, 2022, the National Institutes of Health held a workshop to examine the state of the science concerning obesity interventions in adults to promote health equity. The workshop had three objectives: (1) Convene experts from key institutions and the community to identify gaps in knowledge and opportunities to address obesity, (2) generate recommendations for obesity prevention and treatment to achieve health equity, and (3) identify challenges and needs to address obesity prevalence and disparities, and develop a diverse workforce.

METHODS: A three-day virtual convening.

RESULTS: Several key themes emerged from the workshop discussions that describe directions to build on the currently limited amount of research on obesity, disparities, and equity. Key themes centered on the determinants of health, leveraging technology, clinical, community, commercial, and policy approaches. Community-engaged work, particularly in populations that have received little focus (e.g., sexual gender minorities, Asian communities), were also discussed.

CONCLUSIONS: Future research may be impactful when multilevel approaches are undertaken that leverage equity-minded tools and can be scaled up to meet community-informed population needs in a variety of settings. Funding priorities and workforce development will be critical to realizing health equity.},
}

@article {pmid40926576,
year = {2025},
author = {Achury, R and Staab, M and Seibold, S and Müller, J and Heidrich, L and Püls, M and Hacker, H and Fonseca, CR and Fischer, M and Blüthgen, N and Weisser, W},
title = {Habitat and land-use intensity shape moth community structure across temperate forest and grassland.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70132},
pmid = {40926576},
issn = {1365-2656},
support = {//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Land-use change and intensification are major drivers of biodiversity loss, yet their effects on diversity have usually been studied within a single habitat type or land-use category, limiting our understanding of cross-habitat patterns. Moths, a species-rich taxon worldwide, represent a significant portion of the biodiversity in both temperate forests and grasslands, functioning as pollinators and herbivores. While increasing land-use intensity (LUI) in both habitats is expected to negatively impact moth assemblages, the strength of this effect remains uncertain. Moreover, land-use intensification interacts with broader environmental factors, such as weather conditions and the spread of artificial light at night (ALAN), but their combined effects on moth community diversity and turnover across habitats remain poorly understood. We sampled moth communities across 150 grassland and 150 forest plots along land-use gradients in Germany. We quantified plot- and landscape-scale LUI and tested the role of plant diversity, temperature and precipitation during the night of sampling and the preceding season, and ALAN in shaping moth diversity (standardized by coverage) along Hill numbers. Forests supported significantly higher moth abundance, biomass and diversity than grasslands, with habitat type being the main driver of moth community composition. LUI at the plot scale had contrasting effects on moth abundance, increasing it in forests but reducing it in grasslands. Impacts of LUI were more pronounced at the landscape level, reducing moth diversity particularly in areas dominated by grasslands. Plant diversity and temperature were key determinants for moth communities, increasing alpha diversity across diversity metrics, that is Hill numbers. ALAN had no significant influence on moth abundance or biomass but significantly decreased Simpson diversity. Beta diversity increased with geographic distance, habitat change and LUI but decreased with weather differences among plots. Our results highlight the interplay between LUI, habitat type and abiotic factors in shaping moth communities across large spatial scales. Effective conservation strategies should consider maintaining habitat heterogeneity and promoting plant diversity, particularly in temperate habitats exposed to high land-use intensification.},
}

@article {pmid40921753,
year = {2025},
author = {Wang, F and Xue, M and Zhou, L and Doughty, CE and Ciais, P and Reich, PB and Shang, J and Chen, JM and Liu, J and Green, JK and Hao, D and Tao, S and Su, Y and Liu, L and Xia, J and Wang, H and Yu, K and Zhu, Z and Zhu, P and Li, X and Liu, H and Zeng, Y and Yan, K and Liu, L and Lafortezza, R and Su, Y and Meng, Y and Pan, Y and Yang, X and Fu, YH and He, N and Yuan, W and Chen, X},
title = {Contrasting age-dependent leaf acclimation strategies drive vegetation greening across deciduous broadleaf forests in mid- to high latitudes.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {40921753},
issn = {2055-0278},
abstract = {Increasing leaf area and extending vegetation growing seasons are two primary drivers of global greening, which has emerged as one of the most significant responses to climate change. However, it remains unclear how these two leaf acclimation strategies would vary across forests at a large spatial scale. Here, using multiple satellite-based datasets and field measurements, we analysed the temporal changes (Δ) in maximal leaf area index (LAImax) and length of the growing season (LOS) from 2002 to 2021 across deciduous broadleaf forests (DBFs) in the middle to high latitudes. Contrary to the widely held assumption of coordination, our results revealed a negative correlation between ΔLAImax and ΔLOS. Notably, the trade-offs between ΔLAImax and ΔLOS were strongly explained by stand age. Younger DBFs, with lower baseline LAImax, predominantly located in eastern Asia, displayed an increase in LAImax with small changes in LOS. This acquisitive strategy facilitated younger DBFs to grow more photosynthetically efficient leaves with low leaf mass per area, enhancing their light use efficiency. Conversely, older DBFs with a higher baseline LAImax, primarily located in North America and Europe, extended their LOS by increasing leaf mass per area. This conservative strategy facilitated older DBFs to produce thicker, but less photosynthetically efficient leaves, resulting in decreased light use efficiency. Our findings offer new insights into the contrasting changes in leaf area and growing season length and highlight their divergent impacts on ecosystem functioning.},
}

@article {pmid40920919,
year = {2025},
author = {Li, Y and Meng, L and Richardson, AD and Lee, X and Menzel, A and Mao, J and Diehl, JL and Wang, A},
title = {Cooling outweighs warming across phenological transitions in the Northern Hemisphere.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {37},
pages = {e2501844122},
doi = {10.1073/pnas.2501844122},
pmid = {40920919},
issn = {1091-6490},
mesh = {Seasons ; Forests ; Temperature ; *Climate Change ; *Global Warming ; Plant Leaves/physiology ; Trees ; },
abstract = {Vegetation phenology, i.e., seasonal biological events such as leaf-out and leaf-fall, regulates local climate through biophysical processes like evapotranspiration (ET) and albedo. However, the net surface temperature impact of these processes-whether ET cooling or albedo-induced warming predominates-and how the dominance changes across phenological transitions and regions remains poorly understood. Here, we investigated the effects of vegetation foliage on daytime land surface temperature (LST) following six phenological transitions, spanning from the start of season to end of season, in deciduous and mixed forests across the mid- to high-latitude Northern Hemisphere during 2013-2021 using multiple satellite products and ground observations. We quantified vegetation effect as the difference between observed LST and LST estimates from the Annual Temperature Cycle (ATC) model, representing a no-foliage scenario. We found that vegetation-induced cooling consistently outweighs warming following all phenological transitions except for the end of the season. Cooling intensity increased with vegetation greenness, ranging from 1.0 ± 0.5 °C (mean ± 0.15 SD) in 59% of forests after the start of the season (SOS) to 6.1 ± 0.8 °C in 89% of forests following the onset of maturity, before declining toward the end of the season. Over half of the regions experiencing cooling showed intensification of surface cooling with climate warming, suggesting an amplified vegetation-mediated cooling under future climate change. The findings provide a more precise understanding of the role of vegetation in modulating climate at the intraseasonal scale, highlighting the importance of integrating phenological impacts into climate adaptation strategies and Earth system modeling.},
}

Seasons
Forests
Temperature
*Climate Change
*Global Warming
Plant Leaves/physiology
Trees

@article {pmid40920559,
year = {2025},
author = {Abdugheni, R and Li, WJ},
title = {EzBioCloud 16S rRNA Gene Sequence Formatter: a Python-based sequence formatting tool for systematic microbiology.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.006890},
pmid = {40920559},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/classification/genetics ; *Software ; Sequence Analysis, DNA/methods ; *Computational Biology/methods ; },
abstract = {EzBioCloud is one of the practical reference databases and analytical platforms for systematic microbiology research. The EzBioCloud database provides convenient services in this regard, especially for performing sequence analysis using the 16S rRNA genes. However, '.fasta' files of 16S rRNA sequences obtained after the alignment in EzBioCloud need manual formatting for further analysis and phylogenetic tree construction, which is labourious and time-consuming. To address this issue, we have developed a Python-based tool, EzBioCloud 16S rRNA Gene Sequence Formatter (version 1.0), designed to assist in sequence formatting. Here, we report the development and application of the tool and present this tool publicly to support the researchers in the relevant field.},
}

*RNA, Ribosomal, 16S/genetics
Phylogeny
*Bacteria/classification/genetics
*Software
Sequence Analysis, DNA/methods
*Computational Biology/methods

@article {pmid40920446,
year = {2025},
author = {Jackson, K and Gabrielli, J and Colby, S and Wray, T and Janssen, T and Rogers, M and Delapaix, C},
title = {Real-Time Exposure to Alcohol Content in Digital Media in Adolescents: Protocol for a Multiburst Ecological Momentary Assessment Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e50649},
doi = {10.2196/50649},
pmid = {40920446},
issn = {1929-0748},
mesh = {Humans ; Adolescent ; *Ecological Momentary Assessment ; Male ; Female ; *Social Media/statistics & numerical data ; Prospective Studies ; *Alcohol Drinking/psychology ; *Adolescent Behavior/psychology ; Surveys and Questionnaires ; *Underage Drinking/psychology ; Digital Media ; },
abstract = {BACKGROUND: Digital media frequently contains positive portrayals of alcohol content, which has been shown to be associated with alcohol-related cognitions and behaviors. Because youth are heavy media consumers and have access to unsupervised, repeat viewing of media content on their personal mobile devices, it is critical to understand the frequency of encountering alcohol content in adolescents' daily lives and how adolescents engage with the content.

OBJECTIVE: This paper outlines the study protocol for examining adolescents' exposure to alcohol-related content in digital media within their natural environments.

METHODS: Adolescents (N=302; 31.8% boys, 16.2% nonbinary, 51.3% girls; 25.8% Asian, 3.6% American Indian, 21.5% Black, 4.6% other, 52% White, 25.8% Hispanic or Latinx; mean age 16.21, SD 0.77 y) enrolled in high school were recruited through social media to participate in a prospective study involving bursts of ecological momentary assessment (EMA) reports coupled with longer surveys. We conducted group orientation sessions via videoconference and online surveys, followed by a 21-day EMA period that included scheduled reports across 4 daily time blocks, as well as self-initiated reports on media exposure. Reports of alcohol content exposure included details about the platform, level of engagement, source characteristics, beliefs and perceived norms about the content, the viewing context, and whether the content was sponsored or branded. The participants submitted exposures to alcohol content as an image (screenshot or photo) or text description to be objectively coded. The participants completed a weekly online survey assessing alcohol use and related cognitions. EMA reports will be merged with coded image and text entries and with data from baseline, weekly, and follow-up surveys. Self-reported alcohol exposure will be explored descriptively, and differences in exposure tested across subgroups. Event-level data will be compared with random prompt data to examine differences at times of exposure versus nonexposure. Prospective associations between media alcohol content exposure and alcohol use will be explored over 1-week and 4-month time frames. Mediation of the association between media alcohol exposure and drinking will be tested to explore putative mechanisms.

RESULTS: EMA data collection took place from February 2022 to August 2023. Data management and preliminary analysis are ongoing. Preliminary data were disseminated through conference presentations in 2024-2025 and manuscripts are ongoing with full results anticipated to be published in 2025-2026.

CONCLUSIONS: By characterizing adolescents' real-world exposure to alcohol content in the media, the study provides critical information to develop and implement interventions to target youth behavior that are well suited to delivery via mobile devices. Next steps are to conduct focus groups to understand participants' lived experience of exposure to media alcohol content and reactions to proposed intervention targets. This study and subsequent qualitative work will launch a program of research to counter the effects of alcohol-related media exposure as experienced by adolescents in an effort to minimize underage alcohol involvement.

DERR1-10.2196/50649.},
}

Humans
Adolescent
*Ecological Momentary Assessment
Male
Female
*Social Media/statistics & numerical data
Prospective Studies
*Alcohol Drinking/psychology
*Adolescent Behavior/psychology
Surveys and Questionnaires
*Underage Drinking/psychology
Digital Media

@article {pmid40920239,
year = {2025},
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 = {},
number = {},
pages = {},
pmid = {40920239},
issn = {1861-0692},
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.},
}

@article {pmid40919732,
year = {2025},
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 = {},
number = {},
pages = {},
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/ ; },
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.},
}

@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 {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 {pmid40642868,
year = {2025},
author = {Lopez, MLD and Warren, RL and Allison, MJ and Coombe, L and Imbery, JJ and Birol, I and Helbing, CC},
title = {Conserved Sequence Identification Within Large Genomic Datasets Using 'Unikseq2': Application in Environmental DNA Assay Development.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70014},
pmid = {40642868},
issn = {1755-0998},
support = {//Genome Quebec/ ; //Natural Sciences and Engineering Research Council of Canada/ ; //Genome British Columbia/ ; //Digital Research Alliance of Canada/ ; //Genome Canada/ ; //Liber Ero Foundation/ ; },
mesh = {Animals ; *DNA, Environmental/genetics ; *Conserved Sequence ; *Computational Biology/methods ; Fishes/genetics/classification ; Sequence Analysis, DNA/methods ; *Genomics/methods ; },
abstract = {Identification of conserved genomic sequences and their utilisation as anchor points for clade detection and/or characterisation is a mainstay in ecological studies. For environmental DNA (eDNA) assays, effective processing of large genomic datasets is crucial for reliable species detection in biodiversity monitoring. While considerable focus has been on developing robust species-targeted assays, eDNA assays with broader taxonomic coverage (e.g., detecting any species within a taxonomic group such as fish), can significantly streamline environmental monitoring, especially when detecting individual species' DNA proves challenging. Designing such assays requires identifying conserved regions representing the target taxonomic group, a chiefly manual task that is often labor-intensive and error-prone, particularly when working with large sequence datasets. To address these challenges, we present unikseq2, an enhanced, alignment-free, k-mer-based tool for identifying unique and conserved sequences. It introduces a new functionality to identify sequence conservation among target species, enabling more informed marker selection for applications such as universal primer design. This automates sequence selection in large-scale mitochondrial genome datasets eliminating the need for manual inspection of computationally costly multiple sequence alignments. Herein, we demonstrate unikseq2's capabilities by developing and validating eDNA assays for various taxa, including Osteichthyes (bony fishes), the Salmonidae family (salmon and trout), Myotis bats and Cervus deer. Unikseq2-based eDNA assays allow for accurate detection across multiple taxonomic levels, from genus to class, enhancing the flexibility, scalability and reliability of eDNA tools in environmental monitoring. By leveraging genomic data from public repositories, unikseq2 supports efficient, reproducible assay design, making it an invaluable tool for a wide range of ecological and biodiversity research applications.},
}

Animals
*DNA, Environmental/genetics
*Conserved Sequence
*Computational Biology/methods
Fishes/genetics/classification
Sequence Analysis, DNA/methods
*Genomics/methods

@article {pmid40583840,
year = {2025},
author = {Zhou, H and Tang, J and Cheng, Z and Mei, Y},
title = {InsectTFDB: A Comprehensive Database and Analysis Platform for Insect Transcription Factors.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70006},
doi = {10.1111/1755-0998.70006},
pmid = {40583840},
issn = {1755-0998},
support = {2021YFD1400100//National Key Research and Development Program of China/ ; 2021YFD1400101//National Key Research and Development Program of China/ ; 32102271//National Natural Science Foundation of China/ ; 2022T150579//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Insecta/genetics/classification ; *Transcription Factors/genetics ; *Databases, Genetic ; *Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {Transcription factors (TFs) are key regulators of gene expression, driving diverse biological processes in insects. Despite their importance, a dedicated and comprehensive database for insect TFs has been lacking. To address this gap, we developed InsectTFDB (http://www.insecttfdb.com/), a specialised resource encompassing 1796 insect species across 21 orders, 258 families and 1034 genera. From 59,491,033 predicted proteins, we identified 1,570,627 TFs, systematically classified into six structural groups and annotated using multiple approaches. Approximately 87% of these TFs were successfully annotated to known proteins, enhancing their functional interpretability. InsectTFDB offers a user-friendly interface with four functional modules, including tools for species retrieval, TF exploration, sequence alignment and predictive analysis of novel sequences. These features make it a versatile platform for diverse research applications, from evolutionary studies to functional genomics and pest management. By providing unprecedented taxonomic coverage and reliable annotations, InsectTFDB serves as a critical resource for advancing our understanding of transcriptional regulation and gene regulatory networks across the insects.},
}

Animals
*Insecta/genetics/classification
*Transcription Factors/genetics
*Databases, Genetic
*Computational Biology/methods
Molecular Sequence Annotation

@article {pmid40517927,
year = {2025},
author = {Liu, M and Xie, L and Pan, Y and Li, Y and Zhang, X and Yan, W},
title = {Size-induced toxic effect of plastic particles on earthworms characterized by gut multi-omics analysis.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122133},
doi = {10.1016/j.envres.2025.122133},
pmid = {40517927},
issn = {1096-0953},
mesh = {Animals ; *Oligochaeta/drug effects ; *Soil Pollutants/toxicity ; Particle Size ; *Plastics/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Polystyrenes/toxicity ; Metabolomics ; Nanoparticles/toxicity ; Multiomics ; },
abstract = {The emission and accumulation of plastic particles in soil have raised concerns about their impact on soil organisms. As key components of soil fauna, earthworms (Eisenia fetida) are prone to ingesting plastic particles and experiencing associated health effects. However, the size-dependent toxicological mechanisms of these particles in earthworms remain unclear. In this study, earthworms were exposed to polystyrene particles of different sizes (50 nm, 200 nm, and 250 μm), and their biological responses were evaluated through morphological analysis, gut microbiota profiling, and metabolomics. Micro-sized particles (250 μm, 200 mg kg[-1]) caused mechanical damage to intestinal tissues and reduced survival rates after 28 days. Nano-sized particles (50 nm, 200 nm) disrupted gut microbial diversity and altered metabolic profiles, including reductions in amino acids involved in the TCA cycle. All particle sizes affected metabolite levels and key metabolic pathways. These results indicate that micro-sized particles primarily induce acute physical damage, while nano-sized particles exert long-term biochemical effects. This study highlights the size-specific ecological impacts of plastic particles on soil invertebrates.},
}

Animals
*Oligochaeta/drug effects
*Soil Pollutants/toxicity
Particle Size
*Plastics/toxicity
*Gastrointestinal Microbiome/drug effects
*Polystyrenes/toxicity
Metabolomics
Nanoparticles/toxicity
Multiomics

@article {pmid40505944,
year = {2025},
author = {Liu, F and Lorenz, C and Zhao, G},
title = {From land to sea: Hydrological source tracking of microplastics in coastal sediments.},
journal = {Environmental research},
volume = {283},
number = {},
pages = {122132},
doi = {10.1016/j.envres.2025.122132},
pmid = {40505944},
issn = {1096-0953},
mesh = {*Microplastics/analysis ; *Environmental Monitoring/methods ; *Geologic Sediments/analysis/chemistry ; Denmark ; *Water Pollutants, Chemical/analysis ; Hydrology ; Geographic Information Systems ; },
abstract = {Land-based sources are the predominant contributors to marine microplastic pollution; however, identifying specific inland origins and their correspondence transport paths remain challenging at large-scale. In Denmark, terrestrial-marine connectivity is largely mediated by a complex network of streams, that further complicates hydrological connections between diverse inland discharges and the final coastal receptor. This study presents a GIS-based hydrological source tracking approach to identify the relevant inland discharges and further delineating their transportation paths for microplastics (≥10 μm) sampled from coastal sediments. After analyzed with Focal Plane Array-based Fourier Transform Infrared (FPA-μFTIR) imaging, samples from 13 Danish coastal monitoring stations were tested for souce tracking operations. The tracking tool first screened the stream network across Denmark to identify both point and non-point inland sources-stormwater runoff, wastewater effluent, and combined sewer overflow (CSO)-contributing microplastics to the selected coastal zones. Microplastics were detected at all stations, with variations in abundance, polymer composition, particle shape, and size. Significant positive correlations (p < 0.05) were observed between discharge volume and the composition of certain microplastics: wastewater effluent positively correlates with fiber and polyvinylchloride (PVC), while stormwater-associated discharges (including CSOs) correlated with polypropylene (PP). However, total microplastic concentration was not significantly linked to the discharges. Nevertheless, the GIS-based hydrological tool demonstrated an early-screening tool to identify inland source of marine microplastics. The results underscored the significant role of inland discharges in transporting distinct microplastics to coastal environment, offering valuable insights for authorities to further implement more targeted hydrodynamic modelling, source-specific mitigation strategies, as well as optimised station deployment strategies in future.},
}

*Microplastics/analysis
*Environmental Monitoring/methods
*Geologic Sediments/analysis/chemistry
Denmark
*Water Pollutants, Chemical/analysis
Hydrology
Geographic Information Systems

@article {pmid40304278,
year = {2025},
author = {Lentendu, G and Singer, D and Agatha, S and Bahram, M and Hannula, SE and Helder, J and Tedersoo, L and Traunspurger, W and Geisen, S and Lara, E},
title = {EukFunc: A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e14118},
doi = {10.1111/1755-0998.14118},
pmid = {40304278},
issn = {1755-0998},
support = {PID2021-128499NB-I00 10.13039/501100011033//Ministerio de Ciencia, Innovación y Universidades/ ; 182531//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Soil/parasitology ; *Eukaryota/classification/genetics/physiology ; Animals ; Nematoda/classification/genetics ; *Computational Biology/methods ; Fungi/classification/genetics ; *Soil Microbiology ; },
abstract = {The soil eukaryome constitutes a significant portion of Earth's biodiversity that drives major ecosystem functions, such as controlling carbon fluxes and plant performance. Currently, however, we miss a standardised approach to functionally classify the soil eukaryome in a holistic way. Here we compiled EukFunc, the first functional reference database that characterises the most abundant and functionally important soil eukaryotic groups: fungi, nematodes and protists. We classified the 14,060 species in the database based on their mode of nutrient acquisition into the main functional classes of symbiotroph (40%), saprotroph (26%), phototroph (17%), predator (16%) and unknown (2%). EukFunc provides further detailed information about nutrition mode, including a secondary functional class (i.e., for organisms with multiple nutrition modes), and preyed or associated organisms for predatory or symbiotic taxa, respectively. EukFunc is available in multiple formats for user-friendly functional analyses of specific taxa or annotations of metabarcoding datasets, both embedded in the R package EukFunc. Using a soil dataset from alpine and subalpine meadows, we highlighted the extended ecological insights obtained from combining functional information across the entire soil eukaryome as compared to focusing on fungi, protists or nematodes individually. EukFunc streamlines the annotation process, enhances efficiency and accuracy, and facilitates the investigation of the functional roles of soil eukaryotes-a prerequisite to better understanding soil systems.},
}

*Soil/parasitology
*Eukaryota/classification/genetics/physiology
Animals
Nematoda/classification/genetics
*Computational Biology/methods
Fungi/classification/genetics
*Soil Microbiology

@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 = {},
doi = {10.1093/gigascience/giaf102},
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 {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 {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 {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 = {},
doi = {10.1099/mgen.0.001461},
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 {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},
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 {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 {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 {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 {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 {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 = {},
doi = {10.1093/gigascience/giaf100},
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 {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