@article {pmid40705801,
year = {2025},
author = {Solowiej-Wedderburn, J and Pentz, JT and Lizana, L and Schroeder, BO and Lind, PA and Libby, E},
title = {Competition and cooperation: The plasticity of bacterial interactions across environments.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013213},
pmid = {40705801},
issn = {1553-7358},
mesh = {*Microbial Interactions/physiology ; *Models, Biological ; *Bacteria/genetics/metabolism ; Computational Biology ; Computer Simulation ; *Bacterial Physiological Phenomena ; Metabolic Networks and Pathways/genetics ; Ecosystem ; Environment ; },
abstract = {Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.},
}

*Microbial Interactions/physiology
*Models, Biological
*Bacteria/genetics/metabolism
Computational Biology
Computer Simulation
*Bacterial Physiological Phenomena
Metabolic Networks and Pathways/genetics
Ecosystem
Environment

@article {pmid40705402,
year = {2025},
author = {Oba, T and Takano, K and Sugawara, D and Kimura, K},
title = {Just-in-Time Delivery of Cognitive Behavioral Therapy-Based Exercises: Single-Case Experimental Design With Random Multiple Baselines.},
journal = {JMIR formative research},
volume = {9},
number = {},
pages = {e69556},
pmid = {40705402},
issn = {2561-326X},
mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Female ; Adult ; Male ; Middle Aged ; *Stress, Psychological/therapy/psychology ; *Mobile Applications ; Smartphone ; Single-Case Studies as Topic ; Feasibility Studies ; Japan ; },
abstract = {BACKGROUND: Just-in-time adaptive interventions (JITAIs) are a promising approach in mental health care given the potential scalability (ie, interventions are offered automatically and remotely) and preciseness (ie, the right interventions are offered at the right moments). Typically, a smartphone app is programmed to assess users' psychological states in daily life; when a particular state is detected, the app prompts users to engage in specific behaviors. Conceptually, JITAIs hold significant potential for precision health, although there is currently limited evidence in the literature.

OBJECTIVE: We implemented this scheme as a smartphone intervention for daily stress management, based on cognitive behavioral therapy (CBT), and evaluated its feasibility and efficacy using a single-case experimental design.

METHODS: A total of 8 Japanese adults (community sample: 4 women; mean 37.6, SD 13.1 y) were recruited. An AB phase design with multiple random baselines was used, where "A" represents the baseline phase and "B" represents the intervention phase. Throughout the study period (28 d), participants were prompted to indicate their momentary levels of stress (range 0-100) using a smartphone thrice a day. The baseline phase duration was randomly varied among participants, lasting between 7 and 14 days. The remaining period was used as the intervention phase (14-21 d), where 6 CBT-based exercises (ie, breath control, mindfulness, relaxation, self-talk, cognitive defusion, and cognitive restructuring) were offered depending on the reported levels of stress.

RESULTS: Approximately 70% (6/8) of the participants perceived the intervention to be useful and helpful. A randomization test detected a statistically significant decrease in reported stress levels after the intervention began (P=.005), though this effect was less pronounced when analyzed individually for each participant. Multilevel model analysis detected a significant acute reduction in the momentary level of stress right after completing a CBT-based exercise (pre-exercise: mean 47.98, SD 21.65; post exercise: mean 42.13, SD 19.88; P=.03; Cohen dz=0.58). Also, a significant reduction in depressive rumination was observed in the postintervention assessment (preintervention: mean 13.00, SD 3.21; post intervention: mean 9.25, SD 2.60; P=.01, Cohen dz=1.17).

CONCLUSIONS: The intervention was feasible and effective in reducing subjective stress (and rumination) in the study sample. The small sample size and the nonclinical nature of the sample may limit the generalizability and implications of the study findings for clinical practice. More evidence should be collected to draw solid conclusions for technical and technological as well as clinical aspects of mobile interventions. Accumulating exemplars with different implementations will clarify how a JITAI can be designed and developed on a mobile platform and how the program can be delivered in the prevention and treatment of mental ill health.},
}

Humans
*Cognitive Behavioral Therapy/methods
Female
Adult
Male
Middle Aged
*Stress, Psychological/therapy/psychology
*Mobile Applications
Smartphone
Single-Case Studies as Topic
Feasibility Studies
Japan

@article {pmid40703330,
year = {2025},
author = {Boyes, D and Crowley, LM and Adewumi, T and , and , and , and , and , and , and , },
title = {The genome sequence of the Small Dotted Buff moth, Photedes minima Haworth, 1809.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {299},
pmid = {40703330},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Photedes minima (Small Dotted Buff; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 694.66 megabases. Most of the assembly (99.95%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.38 kilobases.},
}

@article {pmid40702785,
year = {2025},
author = {Lee, TY and Chen, CH and Liu, CM and Chen, IM and Chen, HC and Wu, SI and Hsiao, CK and Kuo, PH},
title = {Fourier Transform Analysis of GPS-Derived Mobility Patterns for Diagnosis and Mood Monitoring of Bipolar and Major Depressive Disorders: Prospective Study.},
journal = {Journal of medical Internet research},
volume = {27},
number = {},
pages = {e71658},
pmid = {40702785},
issn = {1438-8871},
mesh = {Humans ; *Depressive Disorder, Major/diagnosis ; *Bipolar Disorder/diagnosis ; *Geographic Information Systems ; Female ; Male ; Adult ; Prospective Studies ; *Fourier Analysis ; Middle Aged ; Affect ; },
abstract = {BACKGROUND: Mood disorders, including bipolar disorder (BP) and major depressive disorder (MDD), are characterized by significant psychological and behavioral fluctuations, with mobility patterns serving as potential markers of emotional states.

OBJECTIVE: This study explores the diagnostic and monitoring capabilities of Fourier transform, a frequency-domain analysis method, in mood disorders by leveraging GPS data as an objective measure.

METHODS: A total of 62 participants (BP: n=20, MDD: n=27, and healthy controls: n=15) contributed 5177 person-days of data over observation periods ranging from 5 days to 6 months. Key GPS indicators-location variance (LV), transition time (TT), and entropy-were identified as reflective of mood fluctuations and diagnostic differences between BP and MDD.

RESULTS: Fourier transform analysis revealed that the maximum power spectra of LV and entropy differed significantly between BP and MDD groups, with patients with BP exhibiting greater periodicity and intensity in mobility patterns. Notably, participants with BP demonstrated consistent periodic waves (eg, 1-d, 4-d, and 9-d cycles), while such patterns were absent in those with MDD. In addition, after adjusting for age, gender, and employment status, only the power spectrum of LV remained a significant predictor of depressed mood (odds ratio [OR] 0.9976, 95% CI 0.9956-0.9996; P=.02). Daily GPS data showed stronger correlations with ecological momentary assessment (EMA)-reported mood states compared to weekly or monthly aggregations, emphasizing the importance of day-to-day monitoring. Depressive states were associated with reduced LV (OR 0.975, 95% CI 0.957-0.993; P=.008) and TT (OR 0.048, 95% CI 0.012-0.200; P<.001) on weekdays, and lower entropy (OR 0.662, 95% CI 0.520-0.842; P=.001) on weekends, indicating that mobility features vary with social and temporal contexts.

CONCLUSIONS: This study underscores the potential of GPS-derived mobility data, analyzed through Fourier transform, as a noninvasive and real-time diagnostic and monitoring tool for mood disorders. The findings suggest that the intensity of mobility patterns, rather than their frequency, may better differentiate BP from MDD. Integrating GPS data with EMAs could enhance the precision of clinical assessments, provide early warnings for mood episodes, and support personalized interventions, ultimately improving mental health outcomes. This approach represents a promising step toward digital phenotyping and advanced mental health monitoring strategies.},
}

Humans
*Depressive Disorder, Major/diagnosis
*Bipolar Disorder/diagnosis
*Geographic Information Systems
Female
Male
Adult
Prospective Studies
*Fourier Analysis
Middle Aged
Affect

@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}

*Genome, Viral
*RNA Viruses/genetics
Animals
*Computational Biology/methods
Metagenomics/methods
*Software
RNA, Viral/genetics

@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
pmid = {40700599},
issn = {1367-4811},
mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}

*Phylogeny
*Models, Biological
*Microbiota
*Metagenomics/methods
*Computational Biology/methods
Computer Simulation

@article {pmid40522165,
year = {2025},
author = {Huang, JN and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ},
title = {Microplastics Change the Food Utilization of Filter-Feeding Fish via Gut Microbiota.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {15353-15363},
doi = {10.1021/acs.est.5c02067},
pmid = {40522165},
issn = {1520-5851},
mesh = {Animals ; *Carps/growth & development/microbiology/parasitology ; *Environmental Pollutants/toxicity ; Fecal Microbiota Transplantation ; *Feeding Behavior/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Multiomics ; Zebrafish ; Phytoplankton ; Zooplankton ; Food Chain ; },
abstract = {Microplastics (MPs) are ubiquitous in aquatic environments, while their effects on filter-feeding fish are poorly understood. This study aims to explore how MPs change the feeding of planktivorous silver carp. After exposure to MPs, the utilization efficiency of zooplankton by carp increased from 28.45% to 38.63-40.20%, while that of phytoplankton decreased from 50.64% to 40.47-43.32%. MPs did not cause changes in the phytoplankton and zooplankton communities that carp consumed but altered its gut microbiota, leading to increased abundance of genes encoding proteases but decreased carbohydrase genes. Gut metabolomics further showed corresponding metabolic changes especially with increased levels of l-tyrosine, citrulline, succinic acid, and propionic acid, which are significantly correlated with the isotopic signatures of carp utilizing zooplankton. Germ-free zebrafish transplanted with feces of MPs-exposed carp showed metabolic changes like those of carp, verifying that the gut microbiota mediated the effects induced by MPs, while silver carp transplanted with feces of MPs-exposed carp exhibited increased protease activity and enhanced zooplankton utilization efficiency, confirming that MPs could alter its food utilization via gut microbiota. Our findings fill a knowledge gap regarding the ecological risk of MPs to the feeding of planktivorous fish, with potential cascading effects on aquatic ecosystems.},
}

Animals
*Carps/growth & development/microbiology/parasitology
*Environmental Pollutants/toxicity
Fecal Microbiota Transplantation
*Feeding Behavior/drug effects
*Gastrointestinal Microbiome/drug effects
*Microplastics/toxicity
Multiomics
Zebrafish
Phytoplankton
Zooplankton
Food Chain

@article {pmid40699651,
year = {2025},
author = {Wang, H and Zhou, H and Yao, X},
title = {Different Species of Bats: Genomics, Transcriptome, and Immune Repertoire.},
journal = {Current issues in molecular biology},
volume = {47},
number = {4},
pages = {},
pmid = {40699651},
issn = {1467-3045},
support = {82160279//National Natural Science Foundation of China/ ; No. (2018)5637//Guizhou Provincial Hundred level Talent Fund/ ; },
abstract = {Bats are the only mammals with the ability to fly and are the second largest order after rodents, with 20 families and 1213 species (over 3000 subspecies) and are widely distributed in regions around the world except for Antarctica. What makes bats unique are their biological traits: a tolerance to zoonotic infections without getting clinical symptoms, long lifespans, a low incidence of tumors, and a high metabolism. As a result, they are receiving increasing attention in the field of life sciences, particularly in medical research. The rapid advancements in sequencing technology have made it feasible to comprehensively analyze the diverse biological characteristics of bats. This review comprehensively discusses the following: (1) The assembly and annotation overview of 77 assemblies from 54 species across 11 families and the transcriptome sequencing overview of 42 species from 7 families, focused on a comparative analysis of genomic architecture, sensory adaptations (auditory, visual, and olfactory), and immune functions. Key findings encompass marked interspecies divergence in genome size, lineage-specific expansions/contractions of immune-related gene families (APOBEC, IFN, and PYHIN), and sensory gene adaptations linked to ecological niches. Notably, echolocating bats exhibited convergent evolution in auditory genes (SLC26A5 and FOXP2), while fruit-eating bats displayed a degeneration of vision-associated genes (RHO), reflecting trade-offs between sensory specialization and ecological demands. (2) The annotation of the V (variable), D (diversity), J (joining), and C (constant) gene families in the TR and IG loci of 12 species from five families, with a focus on a comparative analysis of the differences in TR and IG genes and CDR3 repertoires between different bats and between bats and other mammals, provides us with a deeper understanding of the development and function of the immune system in organisms. Integrated genomic, transcriptomic, and immune repertoire analyses reveal that bats employ distinct antiviral strategies, primarily mediated by enhanced immune tolerance and suppressed inflammatory responses. This review provides foundational information, collaboration directions, and new perspectives for various laboratories conducting basic and applied research on the vast array of bat biology.},
}

@article {pmid40698863,
year = {2025},
author = {Woo, H and Eyun, SI},
title = {Applications and techniques of single-cell RNA sequencing across diverse species.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40698863},
issn = {1477-4054},
support = {RS-2022-KS221676//Korea Institute of Marine Science & Technology Promotion/ ; RS-2025-02215227//Korea Institute of Marine Science & Technology Promotion/ ; 2022R1A2C4002058//National Research Foundation of Korea/ ; },
mesh = {*Single-Cell Analysis/methods ; Humans ; *Sequence Analysis, RNA/methods ; Animals ; Gene Expression Profiling/methods ; Transcriptome ; Computational Biology/methods ; },
abstract = {Single-cell ribonucleic acid sequencing (scRNA-seq) is an important tool in molecular biology, allowing transcriptomic profiling at the single-cell level. This transformative technology has provided unprecedented insights into cellular heterogeneity, lineage differentiation, and cell-type-specific gene expression patterns, significantly advancing our understanding of complex biological systems. scRNA-seq is broadly applied across various fields, including oncology, where it sheds light on intratumoral heterogeneity and precision medicine strategies, and developmental biology, where it uncovers cellular trajectories in both model and non-model organisms. Additionally, scRNA-seq has been instrumental in ecological genomics, which can help elucidate cellular responses to environmental perturbations and species interactions. Despite these advancements, several challenges remain, particularly technical and financial barriers, limiting its application to non-model organisms and tissues with complex cellular compositions. Addressing these issues will require continued innovation in single-cell isolation methods, cost-effective sequencing technologies, and sophisticated bioinformatics tools. As scRNA-seq advances, it can deepen our understanding of biological systems, with broad implications for personalized medicine, evolutionary biology, and ecological research.},
}

*Single-Cell Analysis/methods
Humans
*Sequence Analysis, RNA/methods
Animals
Gene Expression Profiling/methods
Transcriptome
Computational Biology/methods

@article {pmid40697421,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dark Umber moth, Philereme transversata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {300},
pmid = {40697421},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Philereme transversata (Dark Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence has a total length of 591.75 megabases. Most of the assembly (99.1%) is scaffolded into 20 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.07 kilobases. Gene annotation of this assembly on Ensembl identified 12,207 protein-coding genes.},
}

@article {pmid40694591,
year = {2025},
author = {Gong, R and Feng, Z and Zhang, Y},
title = {Using homologous network to identify reassortment risk in H5Nx avian influenza viruses.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013301},
pmid = {40694591},
issn = {1553-7358},
mesh = {Animals ; *Influenza in Birds/virology/epidemiology ; *Reassortant Viruses/genetics ; *Influenza A virus/genetics ; Birds/virology ; Computational Biology ; Poultry/virology ; Phylogeny ; },
abstract = {The resurgence of H5Nx reassortment has caused multiple epidemics resulting in severe disease even death in wild birds and poultry. Assessing H5Nx reassortment risk is crucial for designing targeted interventions and enhancing preparedness efforts to manage H5Nx outbreaks effectively. However, the complexity in H5Nx reassortment, driven by the diversity of influenza A viruses (IAVs) and wide range of hosts, has hindered the effective quantification of reassortment risk. In this study, we utilized a network approach to explore the reassortment history using a large-scale dataset. By inferring genomic homogeneity among IAVs, we constructed an IAVs homologous network with reassortment history embedded within it. We estimated the communities within the IAVs homologous network to represent the reassortment risk of various viruses, revealing diverse reassortment risks across different H5Nx viruses. Our analysis also identified the primary hosts contributing to reassortment: domestic poultry in China, and wild birds in North America and Europe. These primary hosts are critical targets for future H5Nx reassortment interventions. Our study provides a framework for quantifying and ranking H5Nx reassortment risk, contributing to enhanced preparedness and prevention efforts.},
}

Animals
*Influenza in Birds/virology/epidemiology
*Reassortant Viruses/genetics
*Influenza A virus/genetics
Birds/virology
Computational Biology
Poultry/virology
Phylogeny

@article {pmid40691457,
year = {2025},
author = {Steckler, MR and Kumar, J and Breen, AL and Zhang, T and Hoffman, FM and Hargrove, WW and Walker, DA and Wells, AF and Droghini, A and Nawrocki, TW and Wullschleger, SD and Macander, MJ and Frost, GV and Salmon, VG and Barnett, DT and Iversen, CM},
title = {PAVC: The foundation for a Pan-Arctic Vegetation Cover database.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1271},
pmid = {40691457},
issn = {2052-4463},
mesh = {Arctic Regions ; *Plants/classification ; *Databases, Factual ; Remote Sensing Technology ; Ecosystem ; Trees ; },
abstract = {Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and "other" vegetation, as well as absolute cover for litter and top cover for water and bare ground.},
}

Arctic Regions
*Plants/classification
*Databases, Factual
Remote Sensing Technology
Ecosystem
Trees

@article {pmid40688383,
year = {2025},
author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S},
title = {Analysis of metagenomic data.},
journal = {Nature reviews. Methods primers},
volume = {5},
number = {},
pages = {},
pmid = {40688383},
issn = {2662-8449},
support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; U19 AI174998/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; R35 GM146980/GM/NIGMS NIH HHS/United States ; R01 GM146462/GM/NIGMS NIH HHS/United States ; R01 AI173172/AI/NIAID NIH HHS/United States ; R01 AI100947/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138369/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.},
}

@article {pmid40664368,
year = {2025},
author = {Li, P and Zhu, B and Fu, J and Liu, X and Huang, K and Pan, W and Xue, Q and Zhang, H and Zhang, A and Fu, J and Jiang, G},
title = {Nontarget Screening Analysis Combined with Computational Toxicology: A Promising Solution for Identification and Risk Assessment of Environmental Pollutants in the Big Data Era.},
journal = {Environmental science & technology},
volume = {59},
number = {29},
pages = {14842-14852},
doi = {10.1021/acs.est.4c13225},
pmid = {40664368},
issn = {1520-5851},
mesh = {Risk Assessment ; *Environmental Pollutants ; *Big Data ; *Toxicology ; },
abstract = {Synthetic chemicals are intensively utilized in modern societies, and their mixtures pose significant health and ecological threats. Nontarget screening (NTS) analysis allows for the simultaneous chemical identification and quantitative reporting of tens of thousands of chemicals in complex environmental matrices, whereas the computational toxicology (CT) serves as another high-throughput means of rapidly and comprehensively screening chemicals for toxicity. To date, there has been a lack of guidance on how to combine NTS experiments and CT for the risk assessment of chemical mixtures and the prioritization of pollutants. In this perspective, the combination of two "big data" approaches in field studies is systematically proposed. The basic principles of performing NTS and CT in environmental studies are briefly outlined. The "top-down" and "bottom-up" strategies are proposed to summarize the two technologies during the experimental design stage, in accordance with research objectives and available information and tools. Following this, a universal framework combining NTS and CT is thoroughly explored. Six recommendations for future research are highlighted to enhance the utilization of this paradigm, involving multistep combination, multidisciplinary database, application platform, multilayered functionality, effect validation, and standardization.},
}

Risk Assessment
*Environmental Pollutants
*Big Data
*Toxicology

@article {pmid40583524,
year = {2025},
author = {Kanamori, S and Imamura, K and Inagawa, Y and Yamauchi, T and Ikeda, H and Okuyama, T and Muto, G and Kato, R and Iida, M and Asaoka, H and Inoue, A and Watanabe, K and Tsuno, K and Sasaki, N and Kobayashi, Y and Sakuraya, A and Komase, Y and Otsuka, Y and Iwanaga, M and Inoue, R and Kuribayashi, K and Hino, A and Shimazu, A and Tsutsumi, A and Kawakami, N and Tani, N and Eguchi, H and Kojimahara, N and Ebara, T},
title = {Physical activity interventions delivered through digital health technology for improving workers' mental health symptoms: a systematic review and meta-analysis.},
journal = {Journal of occupational health},
volume = {67},
number = {1},
pages = {},
doi = {10.1093/joccuh/uiaf035},
pmid = {40583524},
issn = {1348-9585},
support = {//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Exercise ; Randomized Controlled Trials as Topic ; *Occupational Health ; *Mental Health ; *Digital Technology ; Depression/prevention & control ; *Health Promotion/methods ; Digital Health ; },
abstract = {OBJECTIVES: This study aimed to clarify the primary preventive effects of physical activity interventions delivered through digital health technology (DHT) on workers' mental health symptoms, and to examine the conditions of attrition and adherence in these interventions.

METHODS: We examined randomized controlled trials (RCTs) that analyzed the effects of physical activity interventions delivered through DHT on workers' health outcomes. We included RCTs published in English or Japanese since 2010 and excluded studies that targeted specific diseases or secondary and tertiary prevention. We conducted the search on July 25, 2023, using Cochrane CENTRAL, Embase, PsycINFO, PubMed, and Ichushi-Web, and citation searches. We assessed risk of bias using the Cochrane Risk of Bias Tool version 2, and data were integrated using a random-effects model. Attrition rates were averaged, and adherence was qualitatively reviewed.

RESULTS: Eight studies were included in the systematic review, and 5 in the meta-analysis. Pooled effect sizes immediately after intervention were as follows: Cohen d = -0.51 (95% CI, -0.75 to -0.27) for depression and negative affect, and -0.36 (95% CI, -0.60 to -0.05) for perceived stress. The attrition rate was 16.8% and 12.4% for the control and intervention groups, with only 2 studies providing details on adherence.

CONCLUSIONS: Physical activity interventions delivered through DHT may moderately improve depression and negative affect, and slightly reduce perceived stress among workers. However, these findings should be interpreted with caution due to the limited number of studies and low evidence certainty. Future studies should explore long-term effects, additional mental health outcomes, and factors affecting adherence.},
}

Humans
*Exercise
Randomized Controlled Trials as Topic
*Occupational Health
*Mental Health
*Digital Technology
Depression/prevention & control
*Health Promotion/methods
Digital Health

@article {pmid40687154,
year = {2025},
author = {Filippova, NV and Zvyagina, EA and Bolshakov, SY and Arefyev, SP and Bulyonkova, TM and Filippov, IV and Rebriev, YA and Shiryaev, AG and Stavishenko, IV and Svetasheva, TY},
title = {Occurrence dataset of protected fungal species for the Red Data Book in Yugra Region, Western Siberia.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e155657},
pmid = {40687154},
issn = {1314-2828},
abstract = {BACKGROUND: The data paper describes a dataset of occurrences of fungal species listed in the Red Data Book of Yugra Region (Western Siberia, Russia). The dataset is based on all digitised records of fungal occurrences in the region. The authors conducted an assessment of the conservation status of fungal species for the revised third edition of the Red Data Book of Yugra. The third edition of the Red Data Book of Yugra includes a total of 61 fungal species (excluding lichens). Of these, nine species are listed on the IUCN Red List and six are included in the Red Data Book of Russia. At the time of publication, the dataset comprises 1180 records of protected species, including human observations, preserved specimens and material citations from literature.

NEW INFORMATION: The paper provides the first overview of the history of fungal conservation in Yugra (Khanty-Mansi Autonomous Okrug-Yugra, KhMAO-Yugra). For the first time, open-source data are used for the assessment of the occurrence of rare species and evaluation of their conservation status for the revised third edition of the Red Data Book of Yugra. An integrated occurrence dataset for the species included in the new edition of the Red Data Book is presented.},
}

@article {pmid40683291,
year = {2025},
author = {Winkler, AS and Brux, CM and Carabin, H and das Neves, CG and Häsler, B and Zinsstag, J and Fèvre, EM and Okello, A and Laing, G and Harrison, WE and Pöntinen, AK and Huber, A and Ruckert, A and Natterson-Horowitz, B and Abela, B and Aenishaenslin, C and Heymann, DL and Rødland, EK and Berthe, FCJ and Capua, I and Sejvar, J and Lubroth, J and Corander, J and May, J and Roth, LF and Thomas, LF and Blumberg, L and Lapinski, MK and Stone, M and Agbogbatey, MK and Xiao, N and Hassan, OA and Dar, O and Daszak, P and Guinto, RR and Senturk, S and Sahay, S and Samuels, TA and Wasteson, Y and Amuasi, JH},
title = {The Lancet One Health Commission: harnessing our interconnectedness for equitable, sustainable, and healthy socioecological systems.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)00627-0},
pmid = {40683291},
issn = {1474-547X},
}

@article {pmid40607556,
year = {2025},
author = {Wu, HW and Gong, CA and Gong, ZN and Zhao, YX and Qiu, HC and Chen, AK},
title = {Monitoring of salt marsh vegetation community succession process in Yellow River Delta supported by multidimensional long time-series feature dataset.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {6},
pages = {1759-1769},
doi = {10.13287/j.1001-9332.202506.029},
pmid = {40607556},
issn = {1001-9332},
mesh = {Chenopodiaceae/growth & development ; China ; Conservation of Natural Resources ; *Environmental Monitoring/methods ; *Poaceae/growth & development ; Population Dynamics ; Rivers ; *Wetlands ; Datasets as Topic ; },
abstract = {The spatial distribution of salt marsh vegetation in Yellow River Delta are highly heterogeneous. Accurate information on the historical distribution of salt marsh is of great significance for regional ecological stability and sustainable development. We constructed a long-series temporal-spatial-spectral multidimensional elicitation based on multi-source data, and accurately extracted information on the spatial distribution of typical salt marsh in the Yellow River Delta from 1996 to 2022 using a random forest (RF) model with recursive feature elimination, and further analyzed the succession of the native/invasive salt marsh communities since the diversion of the Yellow River in 1996. Compared to the single temporal spectral feature, the use of a temporal-spatial-spectral multidimensional feature set for extraction improved the overall accuracy of salt marsh vegetation classification by 8.4%. The classification effect of the sparse Suaeda salsa and the mixed area of Phragmites australis and Spartina alterniflora was optimized based on the temporal and spatial features of optical and SAR images. The distribution of salt marsh on the tidal flats after the Yellow River was diverted was obvious. The cover area of S. salsa communities decreased from 91.67 km[2] in 1996 to 38.11 km[2] in 2022, with the successional trend being influenced by the invasion of S. alterniflora. S. alterniflora was rapidly expanded and then distributed in large areas on the tidal flats on both sides of the current river channel since 2008. The area of the community reached the maximum (51.25 km[2]) in 2020. The invasion and expansion of S. alterniflora had a certain impact on the habitat pattern of the tidal flats.},
}

Chenopodiaceae/growth & development
China
Conservation of Natural Resources
*Environmental Monitoring/methods
*Poaceae/growth & development
Population Dynamics
Rivers
*Wetlands
Datasets as Topic

@article {pmid40367572,
year = {2025},
author = {Wang, H and Li, L and Wu, J and Yuan, X and Hong, L and Pu, L and Qin, S and Li, L and Yang, H and Zhang, J},
title = {Multi-omics analyses reveal differences in intestinal flora composition and serum metabolites in Cherry Valley broiler ducks of different body weights.},
journal = {Poultry science},
volume = {104},
number = {8},
pages = {105275},
pmid = {40367572},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Ducks/microbiology/blood/physiology/growth & development ; *Body Weight ; RNA, Ribosomal, 16S/analysis ; Metabolomics ; *Metabolome ; Male ; Bacteria/classification/isolation & purification ; Multiomics ; },
abstract = {Fledgling broiler ducks vary in body weight and growth rate. The aim of this study was to investigate the relationship between serum metabolites and the intestinal microbiota in Cherry Valley broiler ducks with different finishing weights and to reveal differences in their metabolic regulation and microbial composition. Serum and cecum content samples were collected from Cherry Valley broiler ducks of different finishing weights. Metabolites were identified and compared using untargeted metabolomics, 16S rRNA gene sequencing, multivariate statistics and bioinformatics. Six key findings emerged. First, serum biochemical parameters showed that AST and ALT levels were significantly lower in the high weight group (Group H) than in the low weight group (Group L), and serum immunoglobulin IgG levels were significantly higher in group H. Second, the chorionic height to crypt depth ratio of the duodenum was significantly higher in group H than in group L. Third, the gut microbial community diversity or abundance was lower in broiler ducks in group L. Fourth, LEfSe analysis showed that the biomarker for group L was Streptococcus, whereas for group H it was Faecalibacterium. Fifth, a total of 127 differential metabolites were identified (49 up-regulated and 78 down-regulated). Finally, Spearman's correlation analysis showed that Spearman's correlation analyses showed that the Lipid-related serum metabolites were higher in low-body recombinant broiler ducks, mainly Lathosterol, Cholesterol, Cynaratriol and Leukotriene B4. In addition to lipid-associated serum metabolites in high-body recombination, The water-soluble vitamin-like metabolite Pantothenate and the antibiotic-like metabolite Tylosin were high. The cecum microbiota is strongly associated with metabolites, especially Faecalibacterium, unclassified Tannerellaceae, Subdoligranulum, Alistipes, and [Ruminococcus] torques_group, with which it exhibits strong Correlation. Broiler ducks with higher body weights have a better intestinal villous structure, enhanced digestion and absorption, higher levels of immunoglobulin secretion and superior growth performance. Broiler ducks with different body weights differed in plasma metabolites and cecum flora. Spearman's correlation analyses showed that the Correlation between differential metabolites and differential gut microbial genera.},
}

Animals
*Gastrointestinal Microbiome
*Ducks/microbiology/blood/physiology/growth & development
*Body Weight
RNA, Ribosomal, 16S/analysis
Metabolomics
*Metabolome
Male
Bacteria/classification/isolation & purification
Multiomics

@article {pmid40091737,
year = {2025},
author = {Slipetz, LR and Falk, A and Henry, TR},
title = {Missing Data in Discrete Time State-Space Modeling of Ecological Momentary Assessment Data: A Monte-Carlo Study of Imputation Methods.},
journal = {Multivariate behavioral research},
volume = {60},
number = {4},
pages = {695-710},
doi = {10.1080/00273171.2025.2469055},
pmid = {40091737},
issn = {1532-7906},
mesh = {*Ecological Momentary Assessment ; Humans ; *Monte Carlo Method ; *Models, Statistical ; Data Interpretation, Statistical ; Bias ; Computer Simulation ; Time Factors ; },
abstract = {When using ecological momentary assessment data (EMA), missing data is pervasive as participant attrition is a common issue. Thus, any EMA study must have a missing data plan. In this paper, we discuss missingness in time series analysis and the appropriate way to handle missing data when the data is modeled as an idiographic discrete time continuous measure state-space model. We found that Missing Completely at Random, Missing At Random, and Time-dependent Missing At Random data have less bias and variability than Autoregressive Time-dependent Missing At Random and Missing Not At Random. The Kalman filter excelled at handling missing data under most conditions. Contrary to the literature, we found that using a variety of methods, multiple imputations struggled to recover the parameters.},
}

*Ecological Momentary Assessment
Humans
*Monte Carlo Method
*Models, Statistical
Data Interpretation, Statistical
Bias
Computer Simulation
Time Factors

@article {pmid40680476,
year = {2025},
author = {Roel Lesur, M and Longo, MR and Tajadura-Jiménez, A},
title = {Linking spatial metaphors to body size perception: Different roles of top-down associations and multisensory contributions when mapping auditory cues to finger length.},
journal = {Cortex; a journal devoted to the study of the nervous system and behavior},
volume = {190},
number = {},
pages = {178-191},
doi = {10.1016/j.cortex.2025.06.014},
pmid = {40680476},
issn = {1973-8102},
abstract = {Temporospatial and semantic multisensory aspects contribute to bodily and spatial perception. An informative paradigm to study this is the Auditory Pinocchio Illusion, in which participants perceive an elongation of their finger upon vertically pulling their finger and hearing a concurrent upward pitch glissando. This arguably relies on anchoring (i.e., associating) the ecologically unrelated upward pitch glissando to the finger and allows to separately assess the role of semantic and multisensory contributions. However, what is needed for this anchoring to occur is unknown. In a first Experiment, we manipulated top-down attention to the finger upon which either an ascending or descending sound would be produced. In a second experiment, we compared how different bottom-up multisensory cues (arising from actions performed on the finger) concurrent to the ascending or descending pitch affected finger length perception. Participants either pulled, touched or stretched their finger. Through a perceptual judgment task of finger landmark localization and questionnaire ratings, we measured participants' perceived finger length in both studies and separately assessed their sensory imagery skills. Our results show that attention alters finger length perception according to questionnaire ratings but not perceptual judgements, while concurrent multisensory signals similarly affect both measures. No relationship between these effects and participants' sensory imagery was found. We suggest that while top-down associations between pitch and verticality are necessary and affect questionnaire ratings, they are not sufficient to affect perceptual judgements. Bottom-up somatosensory cues seem to be additionally needed to impact such judgements in this illusion.},
}

@article {pmid40680084,
year = {2025},
author = {Laplane, L and Lamoureux, A and Richker, HI and Marquez Alcaraz, G and Fortunato, A and Shaffer, Z and Aktipis, A and Mischel, PS and Plutynski, A and Townsend, JP and Maley, CC},
title = {Applying multilevel selection to understand cancer evolution and progression.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003290},
doi = {10.1371/journal.pbio.3003290},
pmid = {40680084},
issn = {1545-7885},
abstract = {Natural selection occurs at multiple levels of organization in cancer. At an organismal level, natural selection has led to the evolution of diverse tumor suppression mechanisms, while at a cellular level, it favors traits that promote cellular proliferation, survival and cancer. Natural selection also occurs at a subcellular level, among collections of cells and even among collections of organisms; selection at these levels could influence the evolution of cancer and cancer suppression mechanisms, affecting cancer risk and treatment strategies. There may also be cancer-like processes happening at different levels of organization, in which uncontrolled proliferation at lower levels may disrupt a higher level of organization. This Essay examines how selection operates across levels, highlighting how we might leverage this understanding to improve cancer research, prevention and treatment.},
}

@article {pmid40678991,
year = {2025},
author = {Miller-Ter Kuile, A and Bui, A and Apigo, A and Lamm, S and Swan, M and Sanderlin, JS and Ogle, K},
title = {If You're Rare, Should I Care? How Imperfect Detection Changes Relationships Between Biodiversity and Global Change Drivers.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70362},
doi = {10.1111/gcb.70362},
pmid = {40678991},
issn = {1365-2486},
support = {Challenge Cost Share 21-CS-11221635-194//Rocky Mountain Research Station/ ; },
mesh = {*Biodiversity ; Animals ; Birds ; Plants ; Insecta ; *Climate Change ; Uncertainty ; Conservation of Natural Resources ; },
abstract = {Across ecosystems and biomes, most species in biological communities are rare. Many studies discount rare species when examining biodiversity patterns, assuming that common species are most influential for ecosystem functioning. There is growing evidence, however, that rare species contribute unique functions in many ecosystems; thus, discounting them produces misleading conclusions about how biodiversity is changing in the face of natural and anthropogenic forces. Rare species are more likely to be missed by multi-species sampling designs and are thus particularly vulnerable to detection error. Best practice in biodiversity assessments should include rare species and account for error in the detection process. We outline a general approach that accounts for detection error in sampling designs using multi-species occupancy and abundance models (MSOM/MSAM). We then show how uncertainty in detection can be propagated from MSOM/MSAM results to derive more accurate estimates of alpha and beta diversity metrics. Finally, we show how uncertainty in these diversity metrics can be accounted for in follow-up regression models to evaluate relationships between biodiversity and global change covariates. Using three case studies across diverse taxa (birds, insects, and plants), we demonstrate how accounting for the detection process alters the relationships between biodiversity and global change drivers in ways that are important for understanding and predicting ongoing change in these communities. Our generalizable analysis approach can aid in accounting for rare species in studies of global biodiversity.},
}

*Biodiversity
Animals
Birds
Plants
Insecta
*Climate Change
Uncertainty
Conservation of Natural Resources

@article {pmid40677746,
year = {2025},
author = {Zhou, Y and Trujillo-González, A and Nicol, S and Huerlimann, R and Sarre, SD and Gleeson, D},
title = {Evaluation of DNA barcoding reference databases for marine species in the western and central Pacific Ocean.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19674},
pmid = {40677746},
issn = {2167-8359},
mesh = {*DNA Barcoding, Taxonomic/methods/standards ; Pacific Ocean ; Animals ; *Aquatic Organisms/genetics/classification ; Biodiversity ; Electron Transport Complex IV/genetics ; *Databases, Nucleic Acid/standards ; *Databases, Genetic ; },
abstract = {DNA barcoding is a widely used tool for species identification, with its reliability heavily dependent on reference databases. While the quality of these databases has long been debated, a critical knowledge gap remains in their comprehensive evaluation and comparison at regional scales. Marine metazoan species in the western and central Pacific Ocean (WCPO), a region characterized by high biodiversity and limited sequencing efforts, are an example of this gap. This study developed a systematic workflow to assess mitochondrial cytochrome c oxidase subunit I (COI) barcode coverage and sequence quality in two commonly used reference databases for DNA barcoding: the nucleotide reference database from the National Center for Biotechnology Information (NCBI); and from the Barcode of Life Data System (BOLD). Comparative analyses across marine phyla and WCPO regions identified significant barcode gaps and quality problems, providing insights to guide future barcoding efforts. NCBI exhibited higher barcode coverage, but lower sequence quality compared to BOLD. Quality issues, including over- or under-represented species, short sequences, ambiguous nucleotides, incomplete taxonomic information, conflict records, high intraspecific distances, and low inter-specific distances were identified in both databases, likely resulting from contamination, cryptic species, sequencing errors, or inconsistent taxonomic assignment. The barcode identification number (BIN) system in BOLD demonstrated potential for identifying and addressing problematic records, highlighting the benefits of curated databases. Significant barcode deficiencies and quality issues were observed in the south temperate region of WCPO and phyla such as Porifera, Bryozoa, and Platyhelminthes. Additionally, the COI barcode showed limited species-level resolution for certain taxa, including Scombridae and Lutjanidae. Addressing barcode coverage gaps, improving taxonomic representation, and enhancing sequence quality will be essential for strengthening future barcoding initiatives and advancing biodiversity monitoring and conservation in the WCPO and beyond. This study highlights the need for standardized database curation and sequencing practices to improve the global reliability and applicability of DNA barcoding.},
}

*DNA Barcoding, Taxonomic/methods/standards
Pacific Ocean
Animals
*Aquatic Organisms/genetics/classification
Biodiversity
Electron Transport Complex IV/genetics
*Databases, Nucleic Acid/standards
*Databases, Genetic

@article {pmid40674907,
year = {2025},
author = {Fan, Q and Hu, Y and Huang, S and Guo, Y and Guo, J and Liu, F and Qi, W and Liu, H and Qu, J},
title = {Anti-epidemic pharmaceuticals predominantly contributed to PPCPs flux in the Yangtze River during 2020.},
journal = {Water research},
volume = {286},
number = {},
pages = {124228},
doi = {10.1016/j.watres.2025.124228},
pmid = {40674907},
issn = {1879-2448},
abstract = {The COVID-19 pandemic triggered a surge in pharmaceutical consumption, yet its impact on large-scale riverine systems remains poorly quantified. This study investigated the spatiotemporal distribution, sources and transport flux of 58 pharmaceuticals and personal care products (PPCPs) across the Yangtze River Basin (3400 km mainstream and 8 tributaries) during 2020. The mean concentration of PPCPs was 200.2 ± 205.7 ng/L in 2020, with caffeine (28.2 %), carbamazepine (13.2 %), and metronidazole (9.2 %) as dominant compounds. It was estimated that 449.8 tons of PPCPs were discharged into the sea via the Yangtze River in 2020, of which 48 % (216.0 tons) originated from COVID-19-related pharmaceuticals (e.g., metronidazole, diclofenac). Compared to pre-pandemic levels (2018), the river experienced additional pollution pressure from 209.6 tons of COVID-19 related pharmaceutical emissions. Source apportionment identified post-consumer anthropogenic activities (domestic discharges, clinical effluent outflows, and veterinary applications) as primary contributors (p < 0.05), while industrial sources associated with pharmaceutical production contributed little. Low ecological risks were observed in the study area, likely attributable to high wastewater treatment rates (>90 % in most cities) and the high efficacy of centralized wastewater management. This study provided the first basin-scale quantitative evidence of pandemic-driven PPCP pollution, offering critical insights for balancing public health emergencies with sustainable water resource governance.},
}

@article {pmid40670386,
year = {2025},
author = {McDaniel, JH and Patel, V and Olson, ND and He, HJ and He, Z and Cole, KD and Gooden, AA and Schmitt, A and Sikkink, K and Sedlazeck, FJ and Doddapaneni, H and Jhangiani, SN and Muzny, DM and Gingras, MC and Mehta, H and Behera, S and Paulin, LF and Hastie, AR and Yu, HC and Weigman, V and Rojas, A and Kennedy, K and Remington, J and Salas-González, I and Sudkamp, M and Wiseman, K and Lajoie, BR and Levy, S and Jain, M and Akeson, S and Narzisi, G and Steinsnyder, Z and Reeves, C and Shelton, J and Kingan, SB and Lambert, C and Baybayan, P and Wenger, AM and McLaughlin, IJ and Adamson, A and Kingsley, C and Wescott, M and Kim, Y and Paten, B and Park, J and Violich, I and Miga, KH and Gardner, J and McNulty, B and Rosen, GL and McCoy, R and Brundu, F and Sayyari, E and Scheffler, K and Truong, S and Catreux, S and Hannah, LC and Lipson, D and Benjamin, H and Iremadze, N and Soifer, I and Krieger, G and Eacker, S and Wood, M and Cross, E and Husar, G and Gross, S and Vernich, M and Kolmogorov, M and Ahmad, T and Keskus, AG and Bryant, A and Thibaud-Nissen, F and Trow, J and Proszynski, J and Hirschberg, JW and Ryon, K and Mason, CE and Bhakta, MS and Sanborn, JZ and Munding, EM and Wagner, J and Xiao, C and Liss, AS and Zook, JM},
title = {Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1195},
pmid = {40670386},
issn = {2052-4463},
support = {R35 GM133747/GM/NIGMS NIH HHS/United States ; OT2OD034190//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01HG011274//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; OT2 OD034190/OD/NIH HHS/United States ; 60NANB20D166//United States Department of Commerce | National Institute of Standards and Technology (NIST)/ ; P01 CA272295/CA/NCI NIH HHS/United States ; S10 OD028587/OD/NIH HHS/United States ; U24 HG011853/HG/NHGRI NIH HHS/United States ; R35GM133747//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1936791//National Science Foundation (NSF)/ ; U01CA253405//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54 AG089334/AG/NIA NIH HHS/United States ; R01 CA266279/CA/NCI NIH HHS/United States ; U01 CA253405/CA/NCI NIH HHS/United States ; 1919691//National Science Foundation (NSF)/ ; R01 HG011274/HG/NHGRI NIH HHS/United States ; U24HG011853//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
mesh = {Humans ; Whole Genome Sequencing ; *Genome, Human ; *Pancreatic Neoplasms/genetics ; *Carcinoma, Pancreatic Ductal/genetics ; Cell Line, Tumor ; },
abstract = {The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic dataset from the first individual, HG008, including DNA from an adherent, epithelial-like pancreatic ductal adenocarcinoma (PDAC) tumor cell line and matched normal cells from duodenal and pancreatic tissues. Data for the tumor-normal matched samples comes from seventeen distinct state-of-the-art whole genome measurement technologies, including high depth short and long-read bulk whole genome sequencing (WGS), single cell WGS, Hi-C, and karyotyping. These data will be used by the GIAB Consortium to develop matched tumor-normal benchmarks for somatic variant detection. We expect these data to facilitate innovation for whole genome measurement technologies, de novo assembly of tumor and normal genomes, and bioinformatic tools to identify small and structural somatic variants. This first-of-its-kind broadly consented open-access resource will facilitate further understanding of sequencing methods used for cancer biology.},
}

Humans
Whole Genome Sequencing
*Genome, Human
*Pancreatic Neoplasms/genetics
*Carcinoma, Pancreatic Ductal/genetics
Cell Line, Tumor

@article {pmid40669920,
year = {2025},
author = {Piedboeuf-Potyka, K and Hering, R and Schulz, M and Mackowiak, M and Brinks, R and Kuß, O and Hoyer, A and Tönnies, T},
title = {Incidence of type 2 diabetes by socioeconomic deprivation in Germany between 2014 and 2019: an ecological study.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e094824},
pmid = {40669920},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology ; Germany/epidemiology ; Female ; Male ; Incidence ; Middle Aged ; Aged ; Adult ; *Social Deprivation ; Socioeconomic Factors ; },
abstract = {OBJECTIVE: To estimate type 2 diabetes incidence trends by sex and socioeconomic position (SEP) and evaluate trends in SEP-related inequalities in incidence.

DESIGN: Ecological study using ambulatory claims data and regression-based modelling.

SETTING: All 401 counties in Germany, covering the entire country.

PARTICIPANTS: All individuals with statutory health insurance (~85% of the population). Incident cases of type 2 diabetes were identified annually from 2014 to 2019 using the International Statistical Classification of Diseases and Related Health Problems, 10th revision codes.

Incident type 2 diabetes at the county level, adjusted for age and modelled using a mixed negative binomial regression. SEP was measured using the German Index of Socioeconomic Deprivation, and a random intercept accounted for county-level heterogeneity.

RESULTS: The incidence of type 2 diabetes decreased between 2014 and 2017 and plateaued thereafter. Trends were similar between sexes and deprivation levels. The greatest difference was observed between high and low deprivation, with an incidence rate ratio of 1.20 (95% CI: 1.14 to 1.27) among men and 1.21 (95% CI: 1.14 to 1.27) among women in 2014.

CONCLUSIONS: There was a positive trend in the decline in age-adjusted type 2 diabetes incidence between 2014 and 2019. However, social inequality persisted with deprived groups at higher risk of type 2 diabetes. The level of inequality was comparable between men and women. Continued monitoring is essential to assess whether these short-term trends persist over time.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology
Germany/epidemiology
Female
Male
Incidence
Middle Aged
Aged
Adult
*Social Deprivation
Socioeconomic Factors

@article {pmid40661153,
year = {2025},
author = {Castoe, TA and Daly, M and Jungo, F and Kirchhoff, KN and Koludarov, I and Mackessy, S and Macrander, J and Mehr, S and Modica, MV and Sanchez, EE and Zancolli, G and Holford, M},
title = {A Vision for VenomsBase: An Integrated Knowledgebase for the Study of Venoms and Their Applications.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {7},
number = {1},
pages = {obaf026},
pmid = {40661153},
issn = {2517-4843},
abstract = {Venoms are complex bioactive mixtures that have independently evolved across diverse animal lineages, including snails, insects, sea anemones, spiders, scorpions, and snakes. Despite the growing interest in venom research, data is fragmented across disparate databases which lack standardization and interoperability. A vision for the proposed VenomsBase platform presented here seeks to address these challenges by using the best practices approach in creating a centralized, open-access platform adhering to FAIR principles (Findable, Accessible, Interoperable, and Reproducible). VenomsBase will unify venom datasets, standardize terminology, and enable comparative analyses across species, facilitating novel toxin discovery and functional annotation. Key features of VenomsBase include user-friendly data submission modules with built-in validation, advanced cross-species analysis tools, and integration of multidisciplinary datasets spanning genomics, transcriptomics, proteomics, functional assays, and ecological metadata. A modular, cloud-based design will ensure scalability, while heuristic scoring systems will guide users toward high-confidence data entries. To promote accessibility, the envisioned VenomsBase will provide tutorials, regular training sessions, case studies, and feedback loops, supporting researchers at all levels. By harmonizing venom research and addressing the limitations of outdated or nonstandardized methods, VenomsBase aims to revolutionize the field, while being continuously improved and refined by venom experts. This initiative will unlock venoms' potential to make groundbreaking discoveries, address global health challenges, and foster collaboration and innovation across the scientific community.},
}

@article {pmid40660705,
year = {2025},
author = {Fernando Devasahayam, BR and Uthe, H and Poeschl, Y and Deising, HB},
title = {Confrontations of the Pathogenic Fungus Colletotrichum graminicola With a Biocontrol Bacterium or a Ubiquitous Fungus Trigger Synthesis of Secondary Metabolites With Lead Structures of Synthetic Fungicides.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70145},
pmid = {40660705},
issn = {1462-2920},
support = {//Deutsches Zentrum für integrative Biodiversitätsforschung Halle-Jena-Leipzig/ ; },
mesh = {*Colletotrichum/metabolism/genetics/physiology ; *Fungicides, Industrial/metabolism/chemistry ; Secondary Metabolism ; *Aspergillus nidulans/metabolism/genetics/physiology ; *Bacillus amyloliquefaciens/metabolism/physiology/genetics ; Zea mays/microbiology ; Plant Diseases/microbiology ; Biological Control Agents ; Multigene Family ; },
abstract = {Microbial biological control agents are increasingly used as an alternative to synthetic pesticides. The application of these microorganisms massively affects all members of plant-colonising microbial communities, including pathogenic fungi. In the majority of cases, the resulting competition for ecological niches is decided by the toxicity of microbial secondary metabolites (SMs) formed. In this study, we devised confrontation experiments employing the fungal maize pathogen Colletotrichum graminicola and antagonistic partners, that is the biocontrol bacterium Bacillus amyloliquefaciens and the ubiquitous ascomycete Aspergillus nidulans. Transcriptome studies uncovered strong de-regulation of the vast majority of the C. graminicola secondary metabolite biosynthetic gene clusters (SMBGCs), with 69% and 86% of these clusters de-regulated at confrontation sites with B. amyloliquefaciens or A. nidulans, respectively. In the biocontrol bacterium and in A. nidulans confronting the maize pathogen, 100% and 74% of the SMBGCs were transcriptionally de-regulated, respectively. Correspondingly, non-targeted high-resolution LC-MS/MS revealed a large repertoire of 1738 and 1466 novel features formed in the fungus-bacterium and fungus-fungus confrontation, respectively. Surprisingly, several of these belong to chemical classes with lead structures of synthetic fungicides.},
}

*Colletotrichum/metabolism/genetics/physiology
*Fungicides, Industrial/metabolism/chemistry
Secondary Metabolism
*Aspergillus nidulans/metabolism/genetics/physiology
*Bacillus amyloliquefaciens/metabolism/physiology/genetics
Zea mays/microbiology
Plant Diseases/microbiology
Biological Control Agents
Multigene Family

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40659395,
year = {2025},
author = {Ka, MM and Gaye, ND and Tukakira, J and Kyem, D and Gary-Webb, T and Sattler, L and Jobe, M and Gaye, B},
title = {Trends over time in age-standardised prevalence of cardiometabolic risk factors in Senegal between 1975 and 2021 by sex: an ecological study from the WHO Inequality Data Repository.},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e101323},
pmid = {40659395},
issn = {2044-6055},
mesh = {Humans ; Senegal/epidemiology ; Male ; Female ; Prevalence ; Middle Aged ; *Diabetes Mellitus/epidemiology ; Adult ; *Hypertension/epidemiology ; *Obesity/epidemiology ; *Cardiometabolic Risk Factors ; Sex Factors ; World Health Organization ; Aged ; *Cardiovascular Diseases/epidemiology ; *Tobacco Use/epidemiology/trends ; Young Adult ; Overweight/epidemiology ; Risk Factors ; Adolescent ; Sex Distribution ; },
abstract = {OBJECTIVE: We aimed to analyse the time trends of cardiometabolic risk factors in Senegal from 1975 to 2021.

DESIGN: Ecological study of publicly available data from the WHO Health Inequality Data Repository.

SETTING: Disaggregated datasets from publicly available sources.

PRIMARY OUTCOME: Trends of age-standardised prevalence rates, stratified by sex for tobacco use, obesity, diabetes and hypertension, were analysed for significance.

PARTICIPANTS: Only data from Senegal were included in this study.

RESULTS: Tobacco use decreased in both sexes between 2000 and 2021, from 1.7% to 0.7% (p value 0.04) in females and from 28.1% to 12.8% (p value 0.04) in males. Obesity and overweight increased in both sexes between 1975 and 2016, from 14.2% to 35.9% (p value <0.001) in females and from 7.2% to 19.5% (p value<0.001) in males. Diabetes increased in both sexes between 1980 and 2014, from 4% to 7.3% (p value <0.001) in females and from 3.6% to 7.5% (p value <0.001) in males. Between 1990 and 2019, hypertension increased in females from 39.1% to 42.9% (p value <0.001). The prevalence of hypertension in males first rose from 37.5% to 40.0% (p value <0.001), then decreased to 37.3% (p value 0.013).

CONCLUSION: Our findings highlight changes in cardiometabolic risk factors in Senegal between 1975 and 2020 by sex. While tobacco use declined, rates of obesity, diabetes and hypertension increased. These findings underscore the need for strategies to mitigate this increase in cardiometabolic risk factors and a consequential rise in non-communicable diseases.},
}

Humans
Senegal/epidemiology
Male
Female
Prevalence
Middle Aged
*Diabetes Mellitus/epidemiology
Adult
*Hypertension/epidemiology
*Obesity/epidemiology
*Cardiometabolic Risk Factors
Sex Factors
World Health Organization
Aged
*Cardiovascular Diseases/epidemiology
*Tobacco Use/epidemiology/trends
Young Adult
Overweight/epidemiology
Risk Factors
Adolescent
Sex Distribution

@article {pmid40658737,
year = {2025},
author = {Lundberg, DS and Kersten, S and Mehmetoğlu Boz, E and Pramoj Na Ayutthaya, P and Zhu, W and Poersch, K and Yuan, W and Swartz, S and Müller, D and Bezrukov, I and , and Weigel, D},
title = {A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions.},
journal = {PLoS biology},
volume = {23},
number = {7},
pages = {e3003237},
pmid = {40658737},
issn = {1545-7885},
mesh = {*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism ; *Arabidopsis Proteins/genetics/metabolism ; Plant Diseases/microbiology/genetics/immunology ; Plant Leaves/microbiology/growth & development/genetics/metabolism ; Salicylic Acid/metabolism ; Gene Expression Regulation, Plant ; Disease Resistance/genetics ; Alleles ; Microbiota ; },
abstract = {When wild plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild Arabidopsis thaliana populations maintain significant functional variation at the ACD6 locus, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet they are of smaller stature, their leaves senesce earlier, and they set fewer seeds compared to plants with the standard allele. We hypothesized that ACD6 hyperactivity would not only affect the growth of microbial pathogens but also more generally change leaf microbiome assembly. To test this in an ecologically meaningful context, we compared plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both outdoors and in naturally lit and climate-controlled indoor conditions, taking advantage of near-isogenic lines as well as a natural accession and a CRISPR-edited derivative. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. The genetic precision of CRISPR-edited plants allowed us to conclude that ACD6 genotype had no effect on mature field plants in our setting, despite reproducibly dramatic effects on greenhouse plants. We conclude that additional abiotic and/or microbial signals present outdoors-but not in the greenhouse-greatly modulate ACD6 activity. This raises the possibility that the fitness costs of other commonly studied immune system genes may be grossly misjudged without field studies.},
}

*Arabidopsis/growth & development/genetics/microbiology/immunology/metabolism
*Arabidopsis Proteins/genetics/metabolism
Plant Diseases/microbiology/genetics/immunology
Plant Leaves/microbiology/growth & development/genetics/metabolism
Salicylic Acid/metabolism
Gene Expression Regulation, Plant
Disease Resistance/genetics
Alleles
Microbiota

@article {pmid40656455,
year = {2025},
author = {Komosar, M and Tamburro, G and Graichen, U and Comani, S and Haueisen, J},
title = {Combination of spatial and temporal de-noising and artifact reduction techniques in multi-channel dry EEG.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1576954},
pmid = {40656455},
issn = {1662-4548},
abstract = {INTRODUCTION: Dry electroencephalography (EEG) allows for recording cortical activity in ecological scenarios with a high channel count, but it is often more prone to artifacts as compared to gel-based EEG. Spatial harmonic analysis (SPHARA) and ICA-based methods (Fingerprint and ARCI) have been separately used in previous studies for dry EEG de-noising and physiological artifact reduction. Here, we investigate if the combination of these techniques further improves EEG signal quality. For this purpose, we also introduced an improved version of SPHARA.

METHODS: Dry 64-channel EEG was recorded from 11 healthy volunteers during a motor performance paradigm (left and right hand, feet, and tongue movements). EEG signals were denoised separately using Fingerprint + ARCI, SPHARA, a combination of these two methods, and a combination of these two methods including an improved SPHARA version. The improved version of SPHARA includes an additional zeroing of artifactual jumps in single channels before application of SPHARA. The EEG signal quality after application of each denoising method was calculated by means of standard deviation (SD), signal to noise ratio (SNR), and root mean square deviation (RMSD), and a generalized linear mixed effects (GLME) model was used to identify significant changes of these parameters and quantify the changes in the EEG signal quality.

RESULTS: The grand average values of SD improved from 9.76 (reference preprocessed EEG) to 8.28, 7.91, 6.72, and 6.15 μV for Fingerprint + ARCI, SPHARA, Fingerprint + ARCI + SPHARA, and Fingerprint + ARCI + improved SPHARA, respectively. Similarly, the RMSD values improved from 4.65 to 4.82, 6.32, and 6.90 μV, and the SNR values changed from 2.31 to 1.55, 4.08, and 5.56 dB.

DISCUSSION: Our results demonstrate the different performance aspects of Fingerprint + ARCI and SPHARA, artifact reduction and de-noising techniques that complement each other. We also demonstrated that a combination of these techniques yields superior performance in the reduction of artifacts and noise in dry EEG recordings, which can be extended to infant EEG and adult MEG applications.},
}

@article {pmid40651964,
year = {2025},
author = {Onofri, S and Moeller, R and Billi, D and Balsamo, M and Becker, A and Benvenuto, E and Cassaro, A and Catanzaro, I and Cockell, CS and Desiderio, A and Ellis, T and Gonzáles-Pastor, JE and Hahn, C and Leys, N and Leo, P and Maurel, MC and Pacelli, C and Pavletic, B and Ripa, C and Rothschild, LJ and Surdo, L},
title = {Synthetic biology for space exploration.},
journal = {NPJ microgravity},
volume = {11},
number = {1},
pages = {41},
pmid = {40651964},
issn = {2373-8065},
support = {4000132667/20/NL/CLR/pt//European Space Agency (ESA)/ ; },
abstract = {Human space exploration faces different challenges. Topics like Bioregenerative Life Support Systems, In Situ Resource Utilization, and radiation protection, still require for more suitable solutions to be applied in long-term space exploration. Synthetic biology could be a powerful tool for enabling human exploration of space and planets. This paper explores key topics including resource utilization, life support systems, radiation protection, and human health, providing recommendations for short-, mid-, and long-term advancements in space exploration.},
}

@article {pmid40650501,
year = {2025},
author = {Davies, H and Smyth, S and Pinchbeck, G and Pirmohamed, M and Savory, R and Noble, PJ and Killick, D},
title = {An e-Reporting Tool for Facilitating Submission of Veterinary Adverse Drug Reaction Reports.},
journal = {Journal of veterinary internal medicine},
volume = {39},
number = {4},
pages = {e70173},
pmid = {40650501},
issn = {1939-1676},
support = {204822/z/16/z/WT_/Wellcome Trust/United Kingdom ; VM0541//Veterinary Medicines Directorate/ ; },
mesh = {Animals ; *Adverse Drug Reaction Reporting Systems ; Electronic Health Records ; United Kingdom ; *Veterinary Drugs/adverse effects ; *Veterinary Medicine ; },
abstract = {BACKGROUND: Adverse events (AEs) are under-reported in veterinary medicine. The ability to report AEs directly from the practice management system (PMS) has been suggested to facilitate reporting. The Small Animal Veterinary Surveillance Network (SAVSNET) informatics system provides an opportunity to integrate reporting into the workflow such that reports can be submitted directly to the National Competent Authority, the Veterinary Medicines Directorate (VMD).

OBJECTIVES: Develop an AE reporting form linked to the PMS allowing for pre-population of some fields from the electronic health record (EHR). Analyze the quality of submitted reports.

ANIMALS: Animals attending United Kingdom (UK) first-opinion veterinary practices participating in SAVSNET.

METHODS: An AE "reporting button" was developed and available in the normal clinical workflow for SAVSNET enrolled practices using the Robovet PMS. The button facilitated capture of pertinent information relating to AEs, including the ability to append clinical notes from the associated EHR. After submission, reports were automatically submitted daily to the VMD. Report quality was assessed using an adapted version of the vigiGrade scoring system, which was used to compare the quality of reports submitted to the VMD via standard routes to those submitted via SAVSNET. Assessment of reports submitted via SAVSNET, was conducted twice. First, considering only information contained in the report and second, considering information contained in both the report and associated clinical notes.

RESULTS: Sixty reports were submitted during the first 18 months by 42 different veterinary practices. The quality of SAVSNET reports was significantly improved by information contained within the clinical notes. These reports were more likely to be well-documented than those submitted via standard routes.

Adverse event reports populated using EHR data are well documented and can support efficient reporting of AEs in veterinary medicine.},
}

Animals
*Adverse Drug Reaction Reporting Systems
Electronic Health Records
United Kingdom
*Veterinary Drugs/adverse effects
*Veterinary Medicine

@article {pmid40648098,
year = {2025},
author = {Quisbert-Trujillo, E and Vuillerme, N},
title = {Towards the Operationalization of Health Technology Sustainability Assessment and the Early Eco Design of the Internet of Medical Things.},
journal = {Sensors (Basel, Switzerland)},
volume = {25},
number = {13},
pages = {},
pmid = {40648098},
issn = {1424-8220},
support = {ANR-23-IACL-0006//National Research Agency (ANR), France/ ; ANR-10-AIRT-05//Investissements d'avenir, French program/ ; ANR-15-IDEX-02//Investissements d'avenir, French program/ ; },
mesh = {*Digital Health/economics/ethics ; *Sustainable Development/economics ; Humans ; *Internet of Things/economics/ethics ; },
abstract = {An increasing number of scholars are raising concerns about the sustainability of digital health, calling for action to prevent its harmful effects on the environment. At this point, however, the comprehensive appraisal of emerging technology in the health sector remains theoretically challenging, and highly difficult to implement in practice and in ecological design. Indeed, background factors such as the rapid evolution of technology or effectiveness-efficiency tradeoffs complicate the task of distinguishing the benefits of digital health from its drawbacks, rendering early Health Technology Sustainability Assessment (HTSA) extremely complex. Within this context, the aim of this article is to draw attention to the pragmatism that should be adopted when anticipating the sustainability of technological innovation in the medical field, while simultaneously proposing an assessment framework grounded in a structural and conceptual dissection of the fundamental purpose of smart technologies and the Internet of Medical Things (IoMT). Building on this, we demonstrate how our framework can be strategically applied through a rapid back-of-the-envelope assessment of the economic and ecological balance when introducing IoMT prototypes for treating a specific condition, based on a preliminary simulation of a defined clinical outcome. In this manner, the article presents evidence that challenges two primary hypotheses, and also encourages reflection on the central role of information and its interpretation when addressing key barriers in the HTSA of digital health. Thereby, it contributes to advancing cost-benefit and cost-effectiveness evaluation tools that support eco design strategies and guide informed decision-making regarding the integration of sustainable IoMT systems into healthcare.},
}

*Digital Health/economics/ethics
*Sustainable Development/economics
Humans
*Internet of Things/economics/ethics

@article {pmid40646719,
year = {2025},
author = {Tong, X and Kobayashi, Y and Ikeda, M and Wen, H and Akimoto, S-i and Shigenobu, S},
title = {Draft genome sequences of Buchnera aphidicola from three aphid species (Hemiptera: Aphididae: Eriosomatinae) associated with gall formation on elm trees.},
journal = {Microbiology resource announcements},
volume = {14},
number = {7},
pages = {e0033625},
pmid = {40646719},
issn = {2576-098X},
support = {Special Postdoctoral Researcher Fellowship//RIKEN/ ; 22K20588//Japan Society for the Promotion of Science/ ; 24-IMS-C279//National Institute for Basic Biology/ ; },
abstract = {The Buchnera aphidicola genomes from eriosomatine gall-forming aphids Tetraneura sorini, Tetraneura akinire, and Eriosoma harunire were sequenced, with genome sizes of 533,871, 530,863, and 627,315 bp, respectively. These genomes shed light on Buchnera's role in aphid symbiosis and adaptation.},
}

@article {pmid40646401,
year = {2025},
author = {Cobos, ME and Dunnum, JL and Armién, B and González, P and Juárez, E and Salazar, JR and Cook, JA and Colella, JP},
title = {Selecting Sites for Strategic Surveillance of Zoonotic Pathogens: A Case Study in Panamá.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40646401},
issn = {1612-9210},
support = {ftd06-089//PICANTE (Pathogen Informatics Center for Analysis, Networking, Translation, and Education, US National Science Foundation)/ ; 347998861//Climate Change Capacity Building Program: Research and Public Health Action Award from the Centers for Infectious Diseases/ ; 111130150.501.274//Ministry of Economy and Finance of Panama/ ; FPI-MEF-056//Ministry of Economy and Finance of Panama/ ; PHoEZyTV I-II//Ministry of Economy and Finance of Panama/ ; ftd06-089//Gorgas Memorial Institute of Studies of Health, Secretaria Nacional de Ciencia y Tecnología/ ; },
abstract = {Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography; however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panamá sampled available environments and propose a multistep approach to selecting survey localities in the future. We use > 8000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identify a few key environmental sampling gaps. To refine surveillance strategies, we select a series of "core" historically sampled localities for continued surveillance, supplemented with additional environmentally distinct sites to more completely represent available environments in Panamá. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling of wildlife for zoonotic pathogen surveillance.},
}

@article {pmid40642517,
year = {2025},
author = {Zapata-Bedoya, S and Velandia-González, M and Contreras, M and Ortiz, C and Neira, Y and La Torre, L and García, S and Salas, D and Carrizales, CJ and Echazú Torres, CD and Ojeda Ocampo, JR and Cox, A and Villalta Coro, MG and Hernándes Rocha, TA},
title = {[Validation of satellite estimates for health interventions: use of microcensus data in Bolivia, 2024Validação de estimativas por satélite para intervenções de saúde: o uso de microcensos na Bolívia, 2024].},
journal = {Revista panamericana de salud publica = Pan American journal of public health},
volume = {49},
number = {},
pages = {e71},
pmid = {40642517},
issn = {1680-5348},
abstract = {OBJECTIVE: To provide more accurate population estimates to support the operation of Bolivia's immunization program.

METHODS: This cross-sectional ecological study calculated population estimates using geospatial covariates extracted from Meta Data for Good and WorldPop satellite imagery, and validated them with the results of a microcensus conducted in five Bolivian municipalities.

RESULTS: Of the 6077 buildings identified in satellite images, 4505 residential buildings were found to be occupied. Of these, 3087 (68.52%) agreed to participate in the survey. A total of 17 617 people were expected and 13 397 were enumerated. Field enumeration identified fewer people under 30 years of age and more people over 60 years of age than expected. The Meta images provided excellent matches when analyzing population estimates by sex. Meta matched best with enumeration in rural areas, and WorldPop matched best with enumeration in urban areas.

CONCLUSIONS: This study demonstrates that combining geospatial analysis with microcensus validation can significantly improve health planning, enabling equitable resource distribution and more effective immunization coverage.},
}

@article {pmid40642052,
year = {2025},
author = {Temmerman, M and Peeters, E and Delacroix, C and Arunda, M and Khalid, S and Hanson, C and Ojong, SA},
title = {The impact of implementing the women's reproductive rights agenda on climate change.},
journal = {Frontiers in global women's health},
volume = {6},
number = {},
pages = {1594066},
pmid = {40642052},
issn = {2673-5059},
abstract = {The 1994 International Conference on Population and Development (ICPD) established sexual and reproductive health and rights (SRHR) as foundational to sustainable development. Thirty years later, advancing women's reproductive rights (WRR), encompassing agency, decision-making autonomy, and universal access to family planning-remains critical not only for health and gender equity but also for mitigating environmental degradation. By reducing unintended pregnancies and empowering women to align childbearing with personal and ecological capacity, WRR alleviates ecological stressors such as deforestation while enhancing health resilience in climate-vulnerable communities. Yet, despite well-documented linkages between population dynamics and environmental change, contemporary climate policies and funding mechanisms persistently exclude WRR. This oversight undermines the potential of reproductive justice to enhance climate resilience. Additionally, claims that integrating WRR into climate agendas covertly promotes population control or represses women in low- and middle-income countries are fundamentally misleading. Crucially, research is needed to quantify the specific environmental impacts of WRR, underscoring the urgent need for robust global models to predict and validate these co-benefits. Strengthening this evidence base is imperative to inform policies that integrate WRR indicators into climate financing frameworks, ensuring gender-responsive programming. Bridging this gap requires interdisciplinary collaboration to develop metrics that capture WRR's role in reducing resource consumption and enhancing adaptive capacity. Embedding WRR within climate agendas would harmonize reproductive justice with environmental action, unlocking synergies between gender equity, health resilience, and sustainability. Fulfilling the ICPD's vision demands centering WRR in global climate strategies, thereby advancing a just and livable future for all.},
}

@article {pmid40641609,
year = {2025},
author = {O'Connor, L and Behar, S and Tarrant, S and Stamegna, P and Pretz, C and Wang, B and Savage, B and Scornavacca, T and Shirshac, J and Wilkie, T and Hyder, M and Zai, A and Toomey, S and Mullen, M and Fisher, K and Tigas, E and Wong, S and McManus, DD and Alper, E and Lindenauer, PK and Dickson, E and Broach, JP and Kheterpal, V and Soni, A},
title = {Healthy at Home for COPD: An Integrated Digital Monitoring, Treatment, and Pulmonary Rehabilitation Intervention.},
journal = {BMC digital health},
volume = {3},
number = {},
pages = {},
pmid = {40641609},
issn = {2731-684X},
support = {KL2 TR001455/TR/NCATS NIH HHS/United States ; TL1 TR000145/TR/NCATS NIH HHS/United States ; U54 HL143541/HL/NHLBI NIH HHS/United States ; UL1 TR001453/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of morbidity and mortality in the United States. Frequent exacerbations result in higher use of emergency services and hospitalizations, leading to poor patient outcomes and high costs. The objective of this study is to demonstrate the feasibility of a multimodal, community-based intervention in treating acute COPD exacerbations.

RESULTS: Over 18 months, 1,333 patients were approached and 100 (7.5%) were enrolled (mean age 66, 52% female). Ninety-six participants (96%) remained in the study for the full enrollment period. Fifty-five (55%) participated in tele-pulmonary-rehabilitation. Participants wore the smartwatch for a median of 114 days (IQR 30-210) and 18.9 hours/day (IQR16-20) resulting in a median of 1034 minutes/day (IQR 939-1133). The rate at which participants completed scheduled survey instruments ranged from 78-93%. Nearly all participants (85%) performed COPD ecological momentary assessment at least once with a median of 4.85 recordings during study participation. On average, a 2.48-point improvement (p=0.03) in COPD Assessment Test Score was observed from baseline to study completion. The adherence and symptom improvement metrics were not associated with baseline patient activation measures.

CONCLUSIONS: A multimodal intervention combining preventative care, symptom and biometric monitoring, and MIH services was feasible in adults living with COPD. Participants demonstrated high protocol fidelity and engagement and reported improved quality of life.},
}

@article {pmid40488574,
year = {2025},
author = {Débarre, F and Hensel, Z},
title = {A Critical Reexamination of Recovered SARS-CoV-2 Sequencing Data.},
journal = {Molecular biology and evolution},
volume = {42},
number = {6},
pages = {},
pmid = {40488574},
issn = {1537-1719},
support = {UIDB/04612/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/04612/2020//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*SARS-CoV-2/genetics ; Humans ; Animals ; Chiroptera/virology ; *Genome, Viral ; Genotype ; China ; Sequence Analysis, RNA ; RNA, Viral/genetics ; Datasets as Topic ; },
abstract = {In 2021, Jesse Bloom published a study addressing why the earliest SARS-CoV-2 sequences in Wuhan from late December 2019 were not those most similar to viruses sampled in bats. The study concluded that recovered partial sequences from Wuhan and annotation of Wuhan links for other sequences increased support for one genotype as the progenitor of the SARS-CoV-2 pandemic. However, we show that the collection date for the recovered sequences was January 30, 2020, later than that of hundreds of other SARS-CoV-2 sequences. Mutations in these sequences also exhibit diversity consistent with SARS-CoV-2 sequences collected in late January 2020. Furthermore, we found that Wuhan exposure history was common for early samples, so Bloom's annotation for a single familial cluster does not support that an early genotype was undersampled in Wuhan. Both the recovered partial sequences and additional annotation align with contemporaneous data rather than increase support for a progenitor. Our findings clarify the significance of the recovered sequences and are supported by additional data and analysis published since mid-2021.},
}

*SARS-CoV-2/genetics
Humans
Animals
Chiroptera/virology
*Genome, Viral
Genotype
China
Sequence Analysis, RNA
RNA, Viral/genetics
Datasets as Topic

@article {pmid39631859,
year = {2025},
author = {Suzuki, T and Nagasu, H and Ebara, T and Kagiyama, N and Kishi, T and Yano, Y and Kario, K and Nishiyama, A and Arima, H and Kawai, F and Shibata, S and Node, K and Mizuno, A},
title = {Unraveling the Implications of Digit Bias in Digital Health - A Literature Review.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {64},
number = {14},
pages = {2090-2099},
doi = {10.2169/internalmedicine.4666-24},
pmid = {39631859},
issn = {1349-7235},
mesh = {Humans ; Bias ; *Digital Technology ; Digital Health ; },
abstract = {Digital health, which encompasses digital medicine and therapy, integrates advanced technologies across healthcare. Central to this transformation is 'digitization,' which converts continuous analog data into a discrete digital form. However, this process is challenging. First, digitization inherently has the potential to introduce information loss, thereby diminishing the richness and complexity of data. Second, "digit bias," a cognitive distortion, emerges in the interpretation phase, where individuals' perceptions of and reactions to digital data are intrinsically skewed. There exist two major cognitive biases during digitization process: "digit preferences," where healthcare providers prioritize specific numbers, and "left digit bias" where continuous variables are disproportionately estimated by focusing on the leftmost digit. Although information loss and cognitive biases can cause significant distortions in healthcare, the effects of this "digitization" process have not been adequately quantified, and the accumulation of further evidence in this field is anticipated.},
}

Humans
Bias
*Digital Technology
Digital Health

@article {pmid40623094,
year = {2025},
author = {Morison, C and Stark, D and Huang, W},
title = {Single-cell mutational burden distributions in birth-death processes.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013241},
pmid = {40623094},
issn = {1553-7358},
mesh = {*Single-Cell Analysis/methods ; Humans ; *Neoplasms/genetics ; *Mutation/genetics ; Computational Biology ; *Models, Genetic ; Cell Division/genetics ; },
abstract = {Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.},
}

*Single-Cell Analysis/methods
Humans
*Neoplasms/genetics
*Mutation/genetics
Computational Biology
*Models, Genetic
Cell Division/genetics

@article {pmid40641182,
year = {2025},
author = {Sung, HM and Kim, SH and Kwon, EJ and Jeong, SH and Lee, HM and Kim, YH and Oh, CK},
title = {Single-Cell Transcriptomic Analysis Reveals Hair Cell-Specific Molecular Responses to Polystyrene Nanoplastics in a Zebrafish Embryo Model.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70028},
pmid = {40641182},
issn = {1470-8744},
support = {RS-2023-00301938//NRF/ ; 30-2023003//Pusan National University Yangsan Hospital/ ; },
abstract = {Polystyrene nanoplastics (PSNPs) have emerged as pervasive environmental pollutants with potential toxicological effects on aquatic ecosystems. Their small size, hydrophobicity, and structural stability enable penetration into biological tissues, inducing diverse toxic responses. This study investigates the physiological and molecular impacts of PSNPs on zebrafish embryos using single-cell RNA sequencing and phenotypic analyses. While PS-NP exposure at environmentally relevant concentrations caused no significant changes in survival or overt phenotypes, it led to alterations in cell type proportions and gene expression. Differentially expressed gene (DEG) analysis revealed the upregulation of genes such as col1a1a, fgfbp2b, cytl1, and fstl1a, which were validated in vivo. These genes are associated with extracellular matrix remodeling, immune regulation, and tissue repair, suggesting that PSNPs activate defensive and reparative mechanisms in response to environmental stress. These findings highlight the molecular and cellular responses to PSNP exposure in zebrafish embryos and underscore the importance of evaluating the ecological risks posed by nanoplastics.},
}

@article {pmid40640514,
year = {2025},
author = {Jaman, T and Bhaskar, S and Saikhom, V and Gogoi, RB and Sarma, KK and Aggarwal, SP},
title = {GeoAI-based soil erosion risk assessment in the Brahmaputra River Basin: a synergistic approach using RUSLE and advanced machine learning.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {901},
doi = {10.1007/s10661-025-14314-w},
pmid = {40640514},
issn = {1573-2959},
mesh = {*Environmental Monitoring/methods ; *Machine Learning ; Rivers ; Risk Assessment ; Geographic Information Systems ; *Soil Erosion/statistics & numerical data ; Remote Sensing Technology ; Soil/chemistry ; India ; },
abstract = {Soil erosion is a critical environmental issue in the Brahmaputra River Basin, threatening agricultural productivity, water resources, and ecological balance. This study employs the revised universal soil loss equation (RUSLE) alongside remote sensing, geographic information systems (GIS), and advanced machine learning models like random forest (RF) and gradient boosting (GB) to analyze soil erosion patterns from 2005 to 2024. The analysis revealed that average annual soil loss increased from 15.8 tons/ha/year in 2005 to 25.4 tons/ha/year in 2024, marking a 60.76% rise over two decades. Peak erosion rates were observed in 2020, with localized hotspots recording up to 32,130 tons/ha/year. Spatial analysis from 2005 to 2024 indicated substantial variability, with soil loss values ranging from - 7.024 to 9034 tons/ha in 2005. Topographic influence, quantified using the LS factor, revealed that 47.2% of the basin area has slopes steeper than 16°, significantly contributing to elevated erosion risk. The rainfall erosivity (R-factor) fluctuated throughout the period, peaking at 2305.73 MJ mm/ha h year in 2015 but declining to 799.21 MJ mm/ha h year by 2024, indicating a temporal shift in rainfall patterns. Vegetation cover improvements during this time reduced the mean C-factor from 0.52 to 0.34, though 13.8% of the basin (approximately 3.05 million ha) still falls under high to very high erosion risk zones. RF model predictions achieved an R[2] of 0.915 and RMSE of 4.82, while GB attained an R[2] of 0.952 with RMSE of 3.97, indicating superior predictive performance. These findings underscore the urgent need for targeted soil conservation measures, afforestation programs, and sustainable watershed management. The integration of AI-driven modeling with remote sensing and GIS provides a robust framework for long-term soil erosion monitoring, enabling informed decision-making for climate adaptation in the region.},
}

*Environmental Monitoring/methods
*Machine Learning
Rivers
Risk Assessment
Geographic Information Systems
*Soil Erosion/statistics & numerical data
Remote Sensing Technology
Soil/chemistry
India

@article {pmid40638618,
year = {2025},
author = {Nagel, CL and Chen, S and Allore, HG and Botoseneanu, A and Newsom, JT and Bishop, N and Dorr, DA and Kaye, J and Quiñones, AR},
title = {Longitudinal sequencing of cardiometabolic multimorbidity among older adults and association with subsequent dementia onset.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326309},
pmid = {40638618},
issn = {1932-6203},
mesh = {Humans ; Aged ; Female ; Male ; *Dementia/epidemiology/etiology ; *Multimorbidity ; Longitudinal Studies ; Aged, 80 and over ; *Cardiovascular Diseases/epidemiology/complications ; Cluster Analysis ; },
abstract = {BACKGROUND: Patterns of development of cardiometabolic multimorbidity (CMM) and the impact of specific cardiometabolic disease combinations on cognitive function are not well understood. This study utilizes sequence analysis to describe the ordering and timing of cardiometabolic disease accumulation over a five-year period and to assess both sociodemographic predictors and cognitive outcomes of typical cardiometabolic disease sequences.

METHODS: We analyzed data from the National Health and Aging Trends Study (2011-2022), including respondents aged ≥65 years without CMM or cognitive impairment at baseline (N = 4956). We used sequence analysis with optimal matching and hierarchical cluster analysis to describe temporal patterns of cardiometabolic disease accumulation and to construct a typology by clustering similar sequences. Sociodemographic predictors of CMM cluster membership were assessed using multinomial logistic regression and discrete time survival analysis was used to examine the association of CMM clusters with subsequent dementia development.

RESULTS: 11.8% of respondents developed CMM within 5-years. From a total of 366 distinct cardiometabolic disease sequences, we identified eight cardiometabolic sequence clusters. The first five clusters, "No Cardiometabolic Disease" (N = 2283, 46.1%); "Diabetes Only" (N=642, 13.0%); Heart Disease Only" (N = 297, 6.0%); "MI Only" (N = 145, 2.9%); "Stroke Only" (N = 132, 2.7%), were composed of persons who did not develop CMM over the observation period. The sixth cluster, "Incident CVD with Multimorbidity" (N = 656, 13.2%), was largely composed of persons with no conditions at baseline who developed incident cardiometabolic disease and/or CMM during the observation period (N = 477, 72.7%) and the seventh cluster, "Diabetes Multimorbidity" (N = 333, 6.7%), primarily consisted of persons with diabetes who developed incident CMM. Finally, the eight cluster (N = 468, 9.4%) was characterized by mortality early in the observation period with minimal CMM development during the observation period. Black and Hispanic race/ethnicity, lower wealth, and obesity were associated with increased likelihood of membership in one or both of the clusters characterized by CMM development. We observed increased dementia risk among persons in the Incident CVD with Multimorbidity cluster (HR = 1.32, 95% CI = 1.04-1.67) and the Diabetes MM cluster (HR = 1.88, 95% CI = 1.44,2.44).

CONCLUSIONS: Development of cardiometabolic multimorbidity is more likely among minoritized and/or low-income older adults and is associated with increased risk of subsequent dementia. Targeted approaches to cardiometabolic disease prevention and risk reduction may be an effective means of slowing or preventing the onset of cognitive decline among these groups.},
}

Humans
Aged
Female
Male
*Dementia/epidemiology/etiology
*Multimorbidity
Longitudinal Studies
Aged, 80 and over
*Cardiovascular Diseases/epidemiology/complications
Cluster Analysis

@article {pmid40638150,
year = {2025},
author = {Fujioka, E and Yoshimura, K and Ujino, T and Yoda, K and Fukui, D and Hiryu, S},
title = {High-Resolution GPS Tracking of Perch-Hunting Bats, Rhinolophus nippon, during Nightly Foraging Behavior.},
journal = {Zoological science},
volume = {42},
number = {3},
pages = {249-259},
doi = {10.2108/zs240033},
pmid = {40638150},
issn = {0289-0003},
mesh = {Animals ; *Chiroptera/physiology ; *Feeding Behavior/physiology ; *Geographic Information Systems ; Echolocation ; Flight, Animal ; Male ; },
abstract = {While the echolocation behavior and specialized adaptive auditory system of the greater horseshoe bat (Rhinolophus ferrumequinum) are well documented, comprehensive insights into its wild ecology, especially its detailed nocturnal movements for foraging behavior, remain scarce. Therefore, our objective was to obtain information on the spatiotemporal features of the movements of the Japanese greater horseshoe bat (Rhinolophus nippon), a close relative of R. ferrumequinum, during foraging. Hence, we investigated the nightly flight paths of R. nippon using high-resolution GPS data loggers. Initially, hidden Markov modeling analysis classified bat flight paths into two behavioral patterns: commuting and area-restricted behavior, the latter primarily corresponding to foraging activities. Focusing on foraging behavior along their trajectory, we observed that R. nippon repeatedly foraged with brief stops lasting only a few minutes and an average distance of approximately 300 m between any two foraging sites. Notably, one individual covered a considerable distance (23.6 km) from its roost, possibly because of irregular social behavior during the mating season. Furthermore, for commuting, bats occasionally used forest roads, which were located along the middle of relatively steep slopes. In cases of echolocations with limited detection distances, echoes from the ground and adjacent tree lines offered crucial navigation cues, underscoring the significance of forest roads as nightly movement routes for echolocating bats. Overall, our findings highlight the importance and urgency of ongoing research on bat movement ecology in Japan.},
}

Animals
*Chiroptera/physiology
*Feeding Behavior/physiology
*Geographic Information Systems
Echolocation
Flight, Animal
Male

@article {pmid40270457,
year = {2025},
author = {Selim, S and San, BT and Koc-San, D and Selim, C},
title = {A two-level approach to geospatial identification of optimal pitaya cultivation sites using multi-criteria decision analysis.},
journal = {Journal of the science of food and agriculture},
volume = {105},
number = {11},
pages = {5851-5862},
doi = {10.1002/jsfa.14297},
pmid = {40270457},
issn = {1097-0010},
mesh = {*Fruit/growth & development/chemistry ; Geographic Information Systems ; Decision Support Techniques ; *Cactaceae/growth & development/chemistry ; Soil/chemistry ; Temperature ; },
abstract = {BACKGROUND: Pitaya, also known as dragon fruit, is one of the most popular and expensive fruits in the world. It has been commercially produced since the early 20th century. This plant requires a specific growing environment and ecological conditions, so it is typically cultivated under greenhouse conditions in Türkiye. However, there is a clear need for a comprehensive assessment of outdoor adaptation and/or outdoor growing areas for sustainable yield at the regional scale.

RESULTS: This study presents a multi-criteria decision-making analysis-based geographical information system (GIS) study to identify and evaluate the suitability of outdoor growing areas for pitaya. In this study, eight crucial factors were identified for outdoor pitaya cultivation: temperature, rainfall, soil pH, soil depth, land use capability, altitude, slope and aspect. An analytical hierarchy process was conducted to determine the weights for each parameter, followed by a weighted overlay analysis using GIS tools. The range of weight values was obtained between 0.2748 and 0.0319. The area of the best places for pitaya cultivation was calculated to be 9245.7 ha (11.7%). It was determined that 32.63%, 37.57% and 18.1% of the locations were moderately suitable, less appropriate and unsuitable, respectively.

CONCLUSION: The selection of comparable production sites will be guided by the study. Such suitable site selection studies are extremely significant since the cultivation of the pitaya plant, which has a high commercial value for economically developing countries, will be crucial to the growth of agricultural employment in these nations. Future research will be guided by this study's methodology and analysis strategies. © 2025 Society of Chemical Industry.},
}

*Fruit/growth & development/chemistry
Geographic Information Systems
Decision Support Techniques
*Cactaceae/growth & development/chemistry
Soil/chemistry
Temperature

@article {pmid40634743,
year = {2025},
author = {Zheng, H and Wu, D and Wang, S and Li, X and Jin, LN and Zhao, B and Li, S and Sun, Y and Dong, Z and Wu, Q and Chen, X and Liu, Y and Chen, J and Tian, H and Liu, Q and Jiang, J and Kan, H and He, K and He, H and Chen, C and Zhao, J and Weichenthal, S and Ji, JS and Cohen, AJ and Hao, J and Li, Q},
title = {Control of toxicity of fine particulate matter emissions in China.},
journal = {Nature},
volume = {643},
number = {8071},
pages = {404-411},
pmid = {40634743},
issn = {1476-4687},
mesh = {China ; *Particulate Matter/toxicity/analysis ; Humans ; *Air Pollution/prevention & control/analysis/legislation & jurisprudence/statistics & numerical data/adverse effects ; *Air Pollutants/toxicity/analysis ; Vehicle Emissions/analysis ; Particle Size ; Environmental Exposure/analysis ; },
abstract = {Fine particulate matter (particulate matter with a diameter of 2.5 μm or less; PM2.5) causes millions of premature deaths globally[1], but not all particles are equally harmful[2-4]. Current air-pollution control strategies, prioritizing PM2.5 mass reduction, have provided considerable health benefits but further refinements based on differences in the toxicity of various emission sources may provide greater benefits[5-7]. Here we integrated field measurements with air-quality modelling to assess the unequal toxicities of PM2.5 from various anthropogenic sources. Our findings revealed that the toxicity per unit of PM2.5 mass differed substantially between major sources, differing by up to two orders of magnitude. PM2.5 from solid fuel combustion in residential stoves had the highest toxicity, followed by those from the metallurgy industry, brake wear, diesel vehicles, petrol vehicles, the cement industry and power plants. We further analysed the source contributions of toxicity-adjusted PM2.5 emissions and population exposures in China. From 2005 to 2021, both the PM2.5 mass and relative-potency-adjusted emissions substantially decreased. Although industrial sources contributed 57.5% to the reduction in PM2.5 mass emissions, the reduction in relative potency-adjusted emissions was driven by residential combustion (approximately 80%). Clean-air policies should consider the differing toxicities of PM2.5 when formulating source-specific emission control regulations. This study proposes a cellular toxicity-based framework for PM2.5 reduction that could address the specific health risks in diverse regions, but further epidemiological studies will be required to confirm their relevance to human health outcomes and their application to public policy.},
}

China
*Particulate Matter/toxicity/analysis
Humans
*Air Pollution/prevention & control/analysis/legislation & jurisprudence/statistics & numerical data/adverse effects
*Air Pollutants/toxicity/analysis
Vehicle Emissions/analysis
Particle Size
Environmental Exposure/analysis

@article {pmid40632788,
year = {2025},
author = {Wang, L and Wang, T and Zhang, XW and Lin, XF and Li, J and Liao, JB and Wang, RW},
title = {Evolution of foraging behaviour induces variable complexity-stability relationships in mutualist-exploiter-predator communities.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013245},
pmid = {40632788},
issn = {1553-7358},
mesh = {Animals ; *Predatory Behavior/physiology ; *Models, Biological ; *Biological Evolution ; Population Dynamics ; Ecosystem ; Computational Biology ; *Feeding Behavior/physiology ; *Symbiosis/physiology ; Computer Simulation ; Food Chain ; },
abstract = {Early ecological theory predicts that complex ecological networks are unstable and are unlikely to persist, despite many empirical studies of such complexity in nature. This inconsistency has fascinated ecologists for decades. To resolve the complexity-stability debate, coupling population dynamics and trait dynamics is considered to be an important way to understand the long-term stability of ecological community assemblages. However, we still do not know how eco-evolutionary feedbacks affect the relationship between complexity and stability in ecologically realistic networks with both antagonistic and mutualistic interactions. Here, we explored an adaptive network model to evaluate how the evolution of foraging preference to determine the relationship between network complexity (i.e., connectance) and stability (i.e., community persistence at steady state) in mutualist-exploiter-predator communities (MEST). Our theoretical results showed: (i) adaptive foraging of the top predator contributes to the stability of mutualism and intermediate intensity of foraging adaptations can lead to chaotic dynamics in a four-species MEST community; (ii) the complexity-stability relationship may show positive monotonic, negative monotonic, peaked and double-peaked patterns in general MEST communities, while the double-peaked pattern is only obtained when both the adaptation intensity and interspecific competition are high. Furthermore, model predictions may be consistent with both the negative monotonic pattern revealed in freshwater communities and the peaked pattern revealed in marine communities. Finally, we infer that foraging adaptations of the top predator may alter positive or/and negative feedback loops (trait-mediated indirect effects) to affect the stability of general MEST communities. Our adaptive network framework may provide an effective way to address the complexity-stability debate in real ecosystems.},
}

Animals
*Predatory Behavior/physiology
*Models, Biological
*Biological Evolution
Population Dynamics
Ecosystem
Computational Biology
*Feeding Behavior/physiology
*Symbiosis/physiology
Computer Simulation
Food Chain

@article {pmid40631490,
year = {2025},
author = {Ogle, K and Barber, JJ and Strange, BM and Boone, RD and Formanack, AM and Peltier, DMP},
title = {Identifying the Climate Conditions Associated With Extreme Growth States in Trees Across the Western United States.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70317},
doi = {10.1111/gcb.70317},
pmid = {40631490},
issn = {1365-2486},
support = {2213599//US National Science Foundation Macrosystems Biology and NEON-Enabled Science/ ; //USGS-Southwest Climate Adaptation Science Center/ ; },
mesh = {*Trees/growth & development ; *Climate Change ; United States ; Droughts ; *Cycadopsida/growth & development ; *Magnoliopsida/growth & development ; *Climate ; Seasons ; },
abstract = {Climate extremes-e.g., drought, atmospheric rivers, heat waves-are increasing in severity and frequency across the western United States of America (USA). Tree-ring widths reflect the concurrent and legacy effects of such climate extremes, yet our ability to predict extreme tree growth is often poor. Could tree-ring data themselves identify the most important climate variables driving extreme low- and high-growth states? How does the importance of these climate drivers differ across species and time? To address these questions, we explored the spatial synchrony of extreme low- and high-growth years, the symmetry of climate effects on the probability of low- and high-growth years, and how climate drivers of extreme growth vary across tree species. We compiled ring widths for seven species (four gymnosperms and three angiosperms) from 604 sites in the western USA and classified each annual ring as representing extreme low, extreme high, or nominal growth. We used classification random forest (RF) models to evaluate the importance of 30 seasonal climate variables for predicting extreme growth, including precipitation, temperature, and vapor pressure deficit (VPD) during and up to four years prior to ring formation. For four species (three gymnosperms, one angiosperm) for which climate was predictive of growth, the RF models correctly classified 89%-98% and 80%-95% of low- and high-growth years, respectively. For these species, asymmetric climate responses dominated. Current-year winter hydroclimate (precipitation and VPD) was most important for predicting low growth, but prediction of high growth required multiple years of favorable moisture conditions, and the occurrence of low-growth years was more synchronous across space than high-growth years. Summer climate and temperature (regardless of season) were only weakly predictive of growth extremes. Our results motivate ecologically relevant definitions of drought such that current winter moisture stress exerts a dominant role in governing growth reductions in multiple tree species broadly distributed across the western USA.},
}

*Trees/growth & development
*Climate Change
United States
Droughts
*Cycadopsida/growth & development
*Magnoliopsida/growth & development
*Climate
Seasons

@article {pmid40628867,
year = {2025},
author = {Lee, CT and Ng, CH and Tnah, LH and Ng, KKS and Diway, B and Khoo, E and Lee, SL},
title = {DNA profile database of Koompassia malaccensis in Malaysia and its application in forensic investigation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24504},
pmid = {40628867},
issn = {2045-2322},
support = {05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; 05-03-10-SF1033//Ministry of Agriculture and Food Security Malaysia/ ; },
mesh = {Malaysia ; Microsatellite Repeats/genetics ; *Forensic Genetics/methods ; *Databases, Nucleic Acid ; Humans ; Gene Frequency ; *DNA Fingerprinting/methods ; Databases, Genetic ; Genotype ; },
abstract = {DNA profiling has been an important tool in human forensic for almost four decades, revolutionising criminal investigations. In recent years, it has also been utilised in timber identification and geographical traceability of stolen logs, with notable increase in forensic DNA analysis related to forest crimes, driven by the growing concerns over illegal logging and forest conservation. In this study, DNA profile database for a tropical timber species, Koompassia malaccensis was established, with a total of 1465 samples from 56 locations across Malaysia genotyped using nine short tandem repeat (STR) markers. Based on the results of cluster analyses, the STR database was partitioned into WM (West Malaysia), EM (East Malaysia) and PS (Peat Swamp) Database. Thereafter, each regional/ecological database was characterised for forensic parameters and allele frequencies. Due to weak population differentiation, the percentage of individuals correctly assigned to the population of origin was low. However, the assignment tests to the region of origin were highly accurate (mean = 99.6%). The STR database is robust and has been used to assist the enforcement agencies in the investigation of forest crimes involving K. malaccensis. A case study is presented to demonstrate its application for individual identification in forensic context.},
}

Malaysia
Microsatellite Repeats/genetics
*Forensic Genetics/methods
*Databases, Nucleic Acid
Humans
Gene Frequency
*DNA Fingerprinting/methods
Databases, Genetic
Genotype

@article {pmid40626351,
year = {2025},
author = {Shirakawa, T and Ide, H and Ikehata, Y and Lu, Y and Kinouchi, R and Iwasa, T and Koga, K and Tateishi, S and Fujino, Y and Yasui, T and Horie, S},
title = {Impact of Symptoms of Late-Onset Hypogonadism as a Potential Driver of Presenteeism.},
journal = {American journal of men's health},
volume = {19},
number = {4},
pages = {15579883251343972},
pmid = {40626351},
issn = {1557-9891},
mesh = {Humans ; Male ; *Hypogonadism/epidemiology/diagnosis ; *Presenteeism/statistics & numerical data ; Middle Aged ; Aged ; Adult ; Fatigue/etiology ; Testosterone/blood ; Surveys and Questionnaires ; Erectile Dysfunction ; Age of Onset ; },
abstract = {Presenteeism, defined as attending work despite physical or mental health issues that impair full productivity, is a prevalent concern with significant implications for workplace efficiency and employee well-being. Testosterone, the primary male sex hormone, plays a vital role in sustaining physical energy, cognitive function, and emotional stability-key factors for optimal work performance. This study explores the association between late-onset hypogonadism (LOH) and presenteeism, emphasizing how LOH-related symptoms such as fatigue, reduced libido, erectile dysfunction, and mood disturbances may contribute to reduced workplace productivity. Data from 96 male patients aged 27 to 76 years, who sought treatment at a university hospital for LOH-related symptoms, were analyzed using blood tests and validated questionnaires, including the Aging Males' Symptoms (AMS) scale, Work Functioning Impairment Scale (WFun), and Sexual Health Inventory for Men. Significant correlations were observed between AMS scores and both work functioning impairment and erectile dysfunction, indicating a strong link between LOH symptoms and presenteeism. In addition, symptoms such as fatigue, diminished motivation, and poor sleep quality were identified as exacerbating factors for work-related impairments. The greatest strength of this study lies in its focus on clinically diagnosed LOH patients, a factor that significantly distinguishes it from prior research on presenteeism in general working populations. This study underscores the potential benefits of testosterone replacement therapy, lifestyle modifications, and workplace wellness programs in addressing presenteeism among employees with LOH. Further research is necessary to assess the efficacy of these interventions in mitigating presenteeism and improving employee well-being.},
}

Humans
Male
*Hypogonadism/epidemiology/diagnosis
*Presenteeism/statistics & numerical data
Middle Aged
Aged
Adult
Fatigue/etiology
Testosterone/blood
Surveys and Questionnaires
Erectile Dysfunction
Age of Onset

@article {pmid40623431,
year = {2025},
author = {Wang, L and Liu, N and Zhou, Y and Zheng, F and Jian, S and Liu, X},
title = {Multi-omics analyses provide insights into the molecular basis for salt tolerance of Phyla nodiflora.},
journal = {The Plant journal : for cell and molecular biology},
volume = {123},
number = {1},
pages = {e70325},
doi = {10.1111/tpj.70325},
pmid = {40623431},
issn = {1365-313X},
support = {2021-400//National Key R&D Program of China (Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs)/ ; 32371326//National Natural Science Foundation of China/ ; 32070551//National Natural Science Foundation of China/ ; 2023B1212060046//Science and Technology Planning Project of Guangdong Province/ ; E3330900-01//Science and Technology Projects in Guangzhou/ ; },
mesh = {*Salt Tolerance/genetics ; Genome, Plant/genetics ; Gene Expression Regulation, Plant ; Abscisic Acid/metabolism ; Transcriptome ; Plant Proteins/genetics/metabolism ; Salt Stress ; Salt-Tolerant Plants/genetics ; Genomics ; Multiomics ; },
abstract = {The perennial herbaceous plant, Phyla nodiflora (Verbenaceae), which possesses natural resistance to multiple abiotic stresses, is widely used as a pioneer species in island ecological restoration. Due to the lack of information about its genome, the mechanism underlying its tolerance to environmental stresses, such as salinity, is almost entirely unknown. Here, we report on the high-quality genome of P. nodiflora that is 403.07 Mb in size, and which was assembled and anchored onto 18 pseudo-chromosomes. Genomic synteny revealed that P. nodiflora underwent two whole genome duplication events, which promoted the expansion of genes related to environmental adaptation and the biosynthesis of secondary metabolites. An integrated genomic and transcriptomic analysis suggested that salt stress tolerance in P. nodiflora is associated with the expansion and activated expression of genes related to abscisic acid (ABA) homeostasis and signaling. The expansion of ZEP family genes may contribute to the consistent increase in ABA levels under salt stress. Lysine acetylomic analysis revealed that exposure to salt led to widespread protein deacetylation, with these proteins primarily involved in signal transduction, carbohydrate transport and metabolism, and transcription regulation. Deacetylation of glutathione S-transferase increased enzymatic activities in response to salt-induced oxidative stress. Collectively, the genomic, transcriptomic, and lysine acetylomic analyses provide profound insight into the molecular basis of the adaptation of P. nodiflora to salt stress, and will be helpful to engineer salt-tolerant plants for ecological restoration.},
}

*Salt Tolerance/genetics
Genome, Plant/genetics
Gene Expression Regulation, Plant
Abscisic Acid/metabolism
Transcriptome
Plant Proteins/genetics/metabolism
Salt Stress
Salt-Tolerant Plants/genetics
Genomics
Multiomics

@article {pmid40622159,
year = {2025},
author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB},
title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021425},
doi = {10.1128/msystems.00214-25},
pmid = {40622159},
issn = {2379-5077},
abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.},
}

@article {pmid40622136,
year = {2025},
author = {Fukuta, M and Fukano, S and Maekawa, N and Kobayashi, S and Okamoto, S and Hirano, M and Nio-Kobayashi, J and Kariwa, H and Kawakami, S and Konnai, S and Yoshii, K},
title = {Development of blood-brain barrier-penetrating antibodies for neutralizing tick-borne encephalitis virus in the brain.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0018425},
doi = {10.1128/msphere.00184-25},
pmid = {40622136},
issn = {2379-5042},
abstract = {UNLABELLED: Tick-borne encephalitis virus (TBEV) belongs to the genus Flavivirus and causes tick-borne encephalitis (TBE), a disease characterized by severe neurological symptoms with a high mortality rate. Currently, no specific antiviral treatments have been developed for TBE. The blood-brain barrier (BBB) restricts drug delivery to the central nervous system, posing a major challenge in developing effective therapies targeting TBEV in the brain. In this study, we developed recombinant anti-TBEV antibodies fused with BBB-penetrating rabies virus glycoprotein (RVG) peptides to facilitate their transport across the BBB. The fusion of RVG peptides to the C-terminus of the heavy chain of whole antibodies or single-chain variable fragment had minimal impact on their neutralizing ability against TBEV. The RVG fusion enhanced antibody binding to the surface of a human brain endothelial cell line and increased permeability in an in vitro BBB model. The RVG-fused antibodies exhibited a higher transport efficiency to the brain than the non-fused antibodies following peripheral injection in mice. Notably, the peripheral administration of the RVG-fused whole antibody after viral invasion into the brain significantly neutralized TBEV in the brains of infected mice. These findings suggest that RVG-fused antibodies represent a promising therapeutic strategy for treating TBE once the virus has entered the brain.

IMPORTANCE: Tick-borne encephalitis virus is a neuroinvasive pathogen that causes severe neurologic disease, significantly affecting patients' quality of life. No specific antiviral treatment is available for tick-borne encephalitis caused by virus multiplication in the brain. The delivery of drugs to the brain via peripheral administration is often obstructed by the blood-brain barrier. To develop targeted antiviral therapies for brain infections, we engineered recombinant antibodies capable of crossing the blood-brain barrier via brain-targeted ligands. These antibodies exhibited permeability across the blood-brain barrier in both in vitro and in vivo models and notably effectively neutralized the virus within the brain following peripheral administration. This study is the first to highlight the therapeutic potential of brain-targeted recombinant antibodies after viral entry into the brain, offering a promising pathway for the development of effective antiviral treatments for tick-borne encephalitis.},
}

@article {pmid40441315,
year = {2025},
author = {Zhang, B and Yang, M and Liu, W},
title = {Integrating multi-omics analysis unveils the key mechanisms of PQS-enhanced Algicidal activity in Enterobacter hormaechei F2.},
journal = {Genomics},
volume = {117},
number = {4},
pages = {111060},
doi = {10.1016/j.ygeno.2025.111060},
pmid = {40441315},
issn = {1089-8646},
mesh = {Quorum Sensing/drug effects ; *Enterobacter/genetics/drug effects/metabolism ; *Quinolones/pharmacology/metabolism ; Proteomics ; Metabolomics ; Bacterial Proteins/metabolism/genetics ; Transcriptome ; Multiomics ; },
abstract = {Quorum sensing, as a pivotal bacterial signaling pathway, exhibits substantial potential for regulating algicidal activity. This study pioneers the integration of multi-omics analyses (transcriptomics, proteomics, metabolomics) with phenotypic profiling to systematically unravel the molecular mechanisms underlying Pseudomonas Quinolone Signal (2-heptyl-3-hydroxy-4(1H)-quinolinone, PQS)-enhanced algicidal activity in Enterobacter hormaechei F2. Co-cultivation with PQS triggered marked reductions in algal biomass and chlorophyll-a levels, outperforming traditional approaches. Fourier-transform infrared spectroscopy (FTIR) revealed PQS-induced metabolic disruption and membrane degradation in algal cells. Transcriptomic profiling identified novel regulatory hubs, including upregulated glycolysis (tktA, transketolase), fatty acid degradation (fadE, acyl-CoA dehydrogenase), and chemotaxis (malE, maltose-binding protein) pathways. Proteomics confirmed PQS-driven enrichment of terpenoid precursors, notably DXS synthase (1-deoxy-D-xylulose-5-phosphate synthase), and quorum sensing effectors. Metabolomics highlighted amino acid derivatives (e.g., L-glutamate) and heterocyclic antibiotics as dominant algicidal metabolites. Crucially, multi-omics integration delineated a core network of 46 key nodes (e.g., ribose transporter rbsB, L-glutamate) coordinating energy metabolism, motility, and algicide synthesis. Fatty acid degradation enzymes (e.g., FadE) and flagellar assembly regulators (e.g., FlgK) emerged as previously unrecognized targets, with PQS significantly enhancing bacterial swarming motility (p < 0.01) and biofilm formation. These findings establish the first mechanistic framework linking PQS signaling to algicidal process, demonstrating its role in synchronizing metabolic flux toward terpenoid synthesis while optimizing bacterial-algal interactions. Key pathways-including chemotaxis (malE) and terpenoid biosynthesis (DXS synthase)-provide actionable targets for engineering bioaugmented consortia or precision algicidal formulations. This work advances quorum sensing-driven strategies for sustainable harmful algal bloom (HAB) mitigation, offering scalable solutions for aquaculture and eutrophic water remediation with minimal ecological disruption. By bridging molecular mechanisms to field applications, the study underscores the translational potential of this approach in global water security initiatives.},
}

Quorum Sensing/drug effects
*Enterobacter/genetics/drug effects/metabolism
*Quinolones/pharmacology/metabolism
Proteomics
Metabolomics
Bacterial Proteins/metabolism/genetics
Transcriptome
Multiomics

@article {pmid40620901,
year = {2025},
author = {Schrama, N and Tilman, AR and Vasconcelos, VV},
title = {Majority illusion drives the spontaneous emergence of alternative states in common-pool resource games with network-based information.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112831},
pmid = {40620901},
issn = {2589-0042},
abstract = {Common-pool resources (CPRs), including fisheries and the atmosphere, are critical for ecological, social, and economic sustainability but are easily overused. We use an agent-based model to investigate how social networks shape resource extraction outcomes. Networks with highly visible nodes can create a "majority illusion" in which most users believe high-intensity extraction is dominant, even if it is not. This misperception can push the entire population toward one of two possible states: an abundant, high-welfare resource or a depleted, low-welfare one. Aligning users' environmental impact with their visibility can mitigate this effect and steer the system toward a single, predictable outcome. These results suggest that network-based policies, such as reshaping information flows, particularly targeting high-impact hubs, could help stabilize cooperative behaviors and encourage sustainable management of CPRs, reducing the risk of tragedy-of-the-commons scenarios.},
}

@article {pmid40619084,
year = {2025},
author = {Liu, X and Hu, Z and Gao, J},
title = {Assessment of soil and groundwater pollution risks from coal gangue backfilling: A case study in Inner Mongolia mining areas.},
journal = {Environmental research},
volume = {285},
number = {Pt 1},
pages = {122303},
doi = {10.1016/j.envres.2025.122303},
pmid = {40619084},
issn = {1096-0953},
abstract = {This study evaluates the environmental risks of coal gangue (CG) filling through leaching experiments and numerical simulation methods. The results show that under acidic conditions, the leaching concentration of heavy metals in CG is relatively high, with copper concentration reaching 0.80 mg/L, exceeding Class I discharge standards. Under neutral conditions, the leachate indicators meet national standards. Although the reclaimed soil meets the agricultural land standards, its fertility level is relatively low (soil quality index 0.416), and cadmium, due to its high toxicity coefficient, becomes the primary ecological risk factor. The use of a layered compaction process can effectively control the migration of leachate. Numerical simulations indicate that the maximum migration depth of pollutants is 17 m, with concentrations stabilizing after 2500 days. The high mineralization of groundwater is primarily influenced by the geological background values, and the fluoride contamination plume has a diffusion range of less than 204 m. The study suggests that engineered CG filling reclamation presents controllable environmental risks and resource utilization potential. However, it is important to note that the study has limitations, such as a short monitoring period and uncertainties in the model predictions. It is recommended to conduct long-term field monitoring to comprehensively assess the environmental impact.},
}

@article {pmid40617847,
year = {2025},
author = {Kindt, R and Siddique, I and Dawson, I and John, I and Pedercini, F and Lillesø, JP and Graudal, L},
title = {The Agroforestry Species Switchboard, a global resource to explore information for 107,269 plant species.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1150},
pmid = {40617847},
issn = {2052-4463},
mesh = {*Plants/classification ; *Databases, Factual ; Biodiversity ; Forestry ; },
abstract = {The Agroforestry Species Switchboard is a comprehensive vascular plant database that guides users to information for a particular taxon from a global but fragmented set of resources. Via standardized species names, a user can rapidly determine which among the 59 contributing databases contain information for a species of interest, and understand how this information can be accessed. By providing taxonomic identifiers to World Flora Online, it is straightforward to check for changes in taxonomy. Among the 59 databases referenced, ten covered over 10,000 species, 20 between 1,000 and 10,000 species, and 22 between 100 and 1,000 species. The top ten plant families for species richness across covered databases were the Fabaceae (9,537 species), Asteraceae (6,041), Rubiaceae (4,812), Poaceae (3,947), Myrtaceae (3,544), Euphorbiaceae (2,689), Malvaceae (2,478), Rosaceae (2,374), Lauraceae (2,334) and Lamiaceae (2,107). Information included in the Switchboard distinguishes 54,812 tree-like species, covering most known tree species globally. Among its applications, the Switchboard can assist species selection for ecological restoration projects to synergize biodiversity and human well-being objectives.},
}

*Plants/classification
*Databases, Factual
Biodiversity
Forestry

@article {pmid40617215,
year = {2025},
author = {Jiao, Y and Miao, X and Liu, X and Gao, Y and Guo, J and Liu, C and Wang, L and Qian, T and Wang, X and Hong, S},
title = {Innovative engineering of red-emissive carbon dots for profoundly sensitive and recyclable determination of malachite green in fish tissue.},
journal = {Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy},
volume = {344},
number = {Pt 1},
pages = {126631},
doi = {10.1016/j.saa.2025.126631},
pmid = {40617215},
issn = {1873-3557},
abstract = {Accurate measurement of hazardous synthetic dye is highly attractive for environmental and food safety inspection. Herein, red fluorescent carbon dots (R-CDs) are meticulously engineered by employing Azure A as a fluorophore to optimize the optical characteristics, thereby promoting high-efficiency fluorescence emission at 648 nm. The constructed R-CDs demonstrate excitation-independent characteristics remarkable photostability and superior water solubility. It is encouraging that the developed R-CDs demonstrate a specific response to MG, effectively differentiating it from other substances. The engineered R-CDs demonstrate concentration-responsive fluorescence quenching towards MG, exhibiting rapid response time with a well-defined linear detection range of 0.09-8.21 μM and ultralow detection limit of 24.2 nM. Furthermore, the spike recovery analysis of MG in fish tissue demonstrated robust performance with recoveries of 97.63-106.0 % (RSD <6.37 %), highlighting the analytical reliability for MG identification in aquatic products. The aforementioned results underscore the significant potential of the developed R-CDs for MG detection in aquatic products and bolster their application in food safety inspections.},
}

@article {pmid40612400,
year = {2025},
author = {Te, TT and Boland, MR and Ghadimi, S and Dzierzewski, JM and Alessi, C and Martin, JL and Kremen, S and Bui, AAT and Naeim, A and Fung, CH},
title = {Predicting subjective sleepiness during auditory cognitive testing using voice signaling analysis.},
journal = {Sleep science and practice},
volume = {9},
number = {1},
pages = {19},
pmid = {40612400},
issn = {2398-2683},
abstract = {BACKGROUND: To determine whether objective markers of sleepiness can be collected passively using voice data to detect sleepiness in individuals undergoing testing in situations where sleepiness is not the focal point of assessment. We assessed verbal reaction time (VRT) as a vocalic marker of subjective sleepiness in middle aged and older adults with history of insomnia and benzodiazepine-receptor-agonist (BZRA) use.

METHODS: Adults aged ≥55 without a diagnosis of dementia were recruited from a BZRA deprescribing clinical trial and enrolled in the present study that tested the feasibility of cognitive testing using out-of-office, self-directed mobile apps. Participants' working/episodic memory were assessed through recorded verbal responses to Verbal Paired Associates (VPA) tests, and ecological momentary assessments (EMA) of self-reported sleepiness (1[not at all] to 4[more prominent]). Using a generalized additive model, we examined the association between VRT during VPA testing and self-reported sleepiness, adjusting for demographic, test parameters, caffeine intake, cognition, mood, and BZRA-use (p≤0.05 was considered significant). A stratified k-fold cross-validation/random forest (SKCV/RF) was performed to classify sleepiness levels, adjusting for other variables.

RESULTS: We analyzed 1,513 observations from 16 patients. VRT was operationalized as the time duration between recording start time and first speech epoch. Longer VRTs were positively associated with greater EMA sleepiness (p≤0.05). The SKCV/RF model yielded a mean F1-score of 0.80 ± 0.08 across folds.

CONCLUSIONS: Longer VRTs correlated with greater self-reported sleepiness, indicating that voice data can be used as a marker of sleepiness in patients undergoing cognitive testing in out-of-office settings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s41606-025-00141-y.},
}

@article {pmid40609068,
year = {2025},
author = {Sura, SA and Lloyd-Smith, JO and Fong, P},
title = {Herbivore community function shapes resilience and bistability of coral reefs.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013221},
pmid = {40609068},
issn = {1553-7358},
mesh = {*Coral Reefs ; *Herbivory/physiology ; Animals ; *Fishes/physiology ; *Models, Biological ; Ecosystem ; Seaweed/physiology ; Humans ; Computational Biology ; Conservation of Natural Resources ; },
abstract = {Ecological communities globally are shifting to degraded states, motivating research into attributes supporting resilience or leading to alternative stable states. Coral reef communities are particularly vulnerable as they are facing myriad anthropogenic impacts that contribute to shifts away from coral dominance, motivating much research on whether these shifts are gradual and reversible transitions versus alternative stable states. Empirical studies demonstrate functionally-diverse herbivorous fish communities support coral reef resilience to anthropogenic impacts. However, few coral reef models incorporate herbivore and algal functional groups and quantify their effects on reef resilience and alternative stable states. We built a coral reef model that includes herbivorous fish functional groups and their algal targets and explored how this expansion affects predictions of resilience and alternative stable states under different scenarios of human impacts. We found evenness across the functional groups of herbivores is increasingly important for reef recovery as fishing pressure increases, and recovery is promoted when algal communities begin with more turf than macroalgae. Our findings also highlight that models omitting functional groups that comprise real communities will miss crucial phenomena, such as loss of alternative stable states for browser-dominated communities, or continued presence of alternative stable states in grazer-dominated communities even when fishing pressure is removed entirely. This work advances our ability to understand and predict coral reef resilience and alternative stable states in the Anthropocene, and provides guidance for conservation policy on fishing practices.},
}

*Coral Reefs
*Herbivory/physiology
Animals
*Fishes/physiology
*Models, Biological
Ecosystem
Seaweed/physiology
Humans
Computational Biology
Conservation of Natural Resources

@article {pmid40608756,
year = {2025},
author = {Ma, J and Yang, S and Wu, Q and Hao, X and Cui, B and Su, Z},
title = {Study on the synergies and trade-offs of sectoral water use and their relationship with economic development.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327626},
pmid = {40608756},
issn = {1932-6203},
mesh = {*Economic Development ; China ; *Water Supply/economics ; Agriculture/economics ; *Water Resources/supply & distribution ; *Conservation of Water Resources/economics ; Conservation of Natural Resources ; Industry ; },
abstract = {Water scarcity is dynamic and complex, beyond geophysical stressors and responses, it is critical to also consider how multi-sector, multiscale economic teleconnections mitigate or exacerbate water shortages. This study analyzes the spatial and temporal characteristics of Water Footprint (WF) in China from 2005 to 2022 and their relationship with economic development. The findings reveal an overall increase in China's WF, with the fastest growth observed in the Northwest and Northeast regions. Notably, Heilongjiang, Inner Mongolia, and Xinjiang experienced significant increases, while Zhejiang, Beijing, and Chongqing saw declines. Agricultural water footprint (WFargi) account for the largest share, while industrial water footprint (WFindu) show a decreasing trend, indicating improved water-use efficiency in industry. However, the rise in contamination water footprint (WFcont) and significant spatial disparities in import water footprint (WFimport) and export water footprint (WFexport) highlight the challenges in water resources management. Across different regions, there is a strong synergy between agricultural and ecological water use, while a notable trade-offs exists between industrial and agricultural water use, particularly in the Northeast. The relationship between WF consumption and economic development in China exhibits a phased pattern. From 2011 to 2016, most regions achieved strong decoupling, but from 2017 to 2022, all regions reverted to weak decoupling. This study provides new insights into the relationship between sectoral water use and economic development at regional and provincial levels, contributing to efforts to alleviate water scarcity, enhance water resources management, and promote sustainable economic development.},
}

*Economic Development
China
*Water Supply/economics
Agriculture/economics
*Water Resources/supply & distribution
*Conservation of Water Resources/economics
Conservation of Natural Resources
Industry

@article {pmid40605677,
year = {2025},
author = {Tian, Y and Pang, J},
title = {Revealing the Coupling Coordination Mechanisms between Carbon Efficiency and Carbon Equity: The Evidence in China's Interprovincial Trade.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13889},
pmid = {40605677},
issn = {1520-5851},
abstract = {Effectively balancing carbon efficiency and carbon equity is vital for China's carbon peaking and carbon neutrality goals; however, the relationship between them remains unclear. This study first reveals the coupling coordination mechanisms between carbon efficiency and carbon equity based on Chinese provincial data from 2012 to 2017. We demonstrated that the carbon efficiency and carbon equity exhibited a strong coupling coordination relation (CCR). Carbon efficiency significantly promoted carbon equity and was a major driver of the CCR. With every 1 unit increase in carbon efficiency, carbon equity and the CCR increased by 3.766 to 5.694 units and approximately 1-2 units, respectively, and the positive impact of carbon efficiency on the CCR was approximately 6 to 8 times that of carbon equity. Carbon efficiency, carbon equity, and the CCR worsened between 2012 and 2017, and the bottom 50% of them were mainly concentrated in central and western provinces with abundant natural resources and net inflow of embodied carbon emission. Additionally, we demonstrated that resource dependence hindered carbon efficiency, carbon equity, and the CCR, and the potential transmission pathways were the crowding-out effect on the technology innovation, digital informatization, and advancement of industrial structure.},
}

@article {pmid40605266,
year = {2025},
author = {Herman, C and Barker, BM and Bartelli, TF and Chandra, V and Krajmalnik-Brown, R and Jewell, M and Li, L and Liao, C and McAllister, F and Nirmalkar, K and Xavier, JB and Caporaso, JG},
title = {A review of engraftment assessments following fecal microbiota transplant.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2525478},
pmid = {40605266},
issn = {1949-0984},
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy/microbiology ; Clostridioides difficile/physiology ; Animals ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Fecal Microbiota Transplant (FMT) is a treatment for recurrent Clostridium difficile infections and is being explored for other clinical applications, from alleviating digestive and neurological disorders, to restoring microbiomes impacted by cancer treatment. Quantifying the extent of engraftment following an FMT is important in understanding a recipient's response to treatment. Engraftment and clinical response need to be investigated independently to evaluate an FMT's role (or lack thereof) in achieving a clinical response. Standardized bioinformatics methodologies for quantifying engraftment extent would not only improve assessment and understanding of FMT outcomes, but also facilitate comparison of FMT results and protocols across studies. Here we review FMT studies, integrating three concepts from microbial ecology as framework to discuss how these studies approached assessing engraftment extent: 1) Community Coalescence investigates microbiome shifts following FMT engraftment, 2) Indicator Features tracks specific microbiome features as a signal of engraftment, and 3) Resilience examines how resistant post-FMT recipients' microbiomes are to reverting back to baseline. These concepts explore subtly different questions about the microbiome following FMT. Taken together, they provide holistic insight into how an FMT alters a recipient's microbiome composition and provide a clear framework for quantifying and communicating about microbiome engraftment.},
}

*Fecal Microbiota Transplantation
Humans
*Gastrointestinal Microbiome
*Clostridium Infections/therapy/microbiology
Clostridioides difficile/physiology
Animals
Feces/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40603442,
year = {2025},
author = {Prokop, P and Balcerčík, J and Bonin, P and Thiebaut, G and Provazník, Z and Zvarík, M and Zvaríková, M and Fedor, P},
title = {The effect of fear and compassion on human willingness to protect predators and prey.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {23278},
pmid = {40603442},
issn = {2045-2322},
support = {1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; 1/0211/25//Slovak Grant Agency VEGA/ ; },
mesh = {Humans ; *Fear/psychology ; Female ; Male ; *Empathy ; *Predatory Behavior ; Animals ; Adult ; Young Adult ; Snakes ; Slovakia ; Conservation of Natural Resources ; },
abstract = {Human perception of predators is extremely important because the decline in biodiversity requires greater involvement from the public in species conservation. We conducted an online study in Slovakia with 225 adult participants (151 women; mean age = 24 years), who viewed a series of short videos depicting predator-prey interactions in which the predator either won or lost the encounter. Most of the predators depicted were large mammals (e.g., leopards, lions), one of which was a snake. We examined participants' compassion towards both the predator and prey and their willingness to protect these species. Participants exhibited greater compassion towards predators when they lost, whereas prey received higher compassion scores when they lost than when they won. Prey generally received higher compassion scores than predators. Fear of perceived animals was negatively correlated with compassion for predators and prey. Perceived fear and compassion for both predators and prey were positively correlated with the willingness to protect them (WTP), although these correlations were negative for the majority of predator species. WTP was not significantly influenced by the outcome of the encounter. Snakes, often considered prototypical stimuli for human fear, elicited less compassion and lower WTP compared to mammalian predators. We conclude that human sensitivity to physical interactions between predators and prey does not necessarily translate into a willingness to protect these animals. Conservation strategies need to consider the emotional and cognitive biases people hold toward different species. By acknowledging these biases, especially fear and perceived charisma, conservation campaigns may more effectively foster public support for protecting a broader range of species.},
}

Humans
*Fear/psychology
Female
Male
*Empathy
*Predatory Behavior
Animals
Adult
Young Adult
Snakes
Slovakia
Conservation of Natural Resources

@article {pmid40600126,
year = {2025},
author = {Boyes, D and , and , and , and , and , and , and , },
title = {The genome sequence of the Dotted Ermel moth, Ethmia dodecea (Haworth, 1828).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {93},
pmid = {40600126},
issn = {2398-502X},
abstract = {We present a genome assembly from a male Ethmia dodecea (Dotted Ermel; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence has a total length of 457.55 megabases. Most of the assembly (99.87%) is scaffolded into 29 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.34 kilobases in length.},
}

@article {pmid40571725,
year = {2025},
author = {Li, X and Liu, W and Shi, R and Ge, Y and Wang, Q and Yin, C and Liu, J and Shi, X and Mo, F and Chen, C and An, J},
title = {6PPD and 6PPD-Q Inhibit Macrophyte Photosynthesis by Targeting Photosynthetic Antenna: Multiomics and Computational Modeling Insights.},
journal = {Environmental science & technology},
volume = {59},
number = {26},
pages = {13216-13226},
doi = {10.1021/acs.est.5c03958},
pmid = {40571725},
issn = {1520-5851},
mesh = {*Photosynthesis/drug effects ; Molecular Docking Simulation ; *Phenylenediamines/toxicity ; Multiomics ; Benzoquinones ; },
abstract = {Emerging evidence indicates that N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and its derivative 6PPD-quinone (6PPD-Q) exert photosynthetic toxicity on aquatic macrophytes. However, their precise inhibitory mechanisms and toxic targets within the photosynthetic pathways remain poorly understood. Through a combination of physio-biochemical indicators, multiomics analysis, and molecular docking simulation, this study systematically explored the photosynthetic toxic effects of 6PPD and 6PPD-Q on Ceratophyllum demersum L. (C. demersum). Transcriptomic data identified photosynthetic antenna proteins as primary molecular targets, with both contaminants perturbing the transcriptional regulation of genes and impairing the structural plasticity of associated proteins. These molecular perturbations consequently disrupted the photosynthetic electron transport efficiency. Metabolomic evidence revealed subsequent carbohydrate metabolism imbalances, suggesting compromised carbon fixation capacity of C. demersum. Additionally, molecular docking simulations demonstrated superior binding affinities for both compounds with antenna proteins, particularly emphasizing the enhanced interactions mediated by 6PPD-Q's quinone structure. Comparative analysis indicated that 6PPD-Q's structural modifications may confer greater photosynthetic toxicity compared to the parent compound 6PPD. This multiomics investigation reveals the mechanistic basis of 6PPD and 6PPD-Q-driven photosynthetic toxicity and underscores their potential to destabilize aquatic ecosystems by disrupting primary productivity.},
}

*Photosynthesis/drug effects
Molecular Docking Simulation
*Phenylenediamines/toxicity
Multiomics
Benzoquinones

@article {pmid40563242,
year = {2025},
author = {Arhami, O and Rohani, P},
title = {Topolow: a mapping algorithm for antigenic cross-reactivity and binding affinity assays.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
doi = {10.1093/bioinformatics/btaf372},
pmid = {40563242},
issn = {1367-4811},
support = {75N93021C00018/AI/NIAID NIH HHS/United States ; //NIAID Centers of Excellence for Influenza Research and Response, CEIRR/ ; },
mesh = {*Algorithms ; Cross Reactions ; Influenza A Virus, H3N2 Subtype/immunology ; *Antigens, Viral/immunology/chemistry ; Dengue Virus/immunology ; HIV/immunology ; Humans ; *Computational Biology/methods ; *Antigens/immunology/chemistry ; },
abstract = {MOTIVATION: Understanding antigenic evolution through cross-reactivity assays is crucial for tracking rapidly evolving pathogens requiring regular vaccine updates. However, existing cartography methods, commonly based on multidimensional scaling (MDS), face significant challenges with sparse and complex data, producing incomplete and inconsistent maps. There is an urgent need for robust computational methods that can accurately map antigenic relationships from incomplete experimental data while maintaining biological relevance, especially given that more than 95% of possible measurements could be missing in large-scale studies.

RESULTS: We present Topolow, an algorithm that transforms cross-reactivity and binding affinity measurements into accurate positions in a phenotype space. Using a physics-inspired model, Topolow achieved comparable prediction accuracy to MDS for H3N2 influenza and 56% and 41% improved accuracy for dengue and HIV, while maintaining complete positioning of all antigens. The method effectively reduces experimental noise and bias, determines optimal dimensionality through likelihood-based estimation, avoiding distortions due to insufficient dimensions, and demonstrates orders of magnitude better stability across multiple runs. We also introduce antigenic velocity vectors, which measure the rate of antigenic advancement of each isolate per unit of time against its temporal and evolutionary related background, revealing the underlying antigenic relationships and cluster transitions.

Topolow is implemented in R and freely available at https://doi.org/10.5281/zenodo.15620983 and https://github.com/omid-arhami/topolow.},
}

*Algorithms
Cross Reactions
Influenza A Virus, H3N2 Subtype/immunology
*Antigens, Viral/immunology/chemistry
Dengue Virus/immunology
HIV/immunology
Humans
*Computational Biology/methods
*Antigens/immunology/chemistry

@article {pmid40598319,
year = {2025},
author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C},
title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {155},
pmid = {40598319},
issn = {2049-2618},
support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; },
mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.},
}

Phylogeny
*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
Metagenomics/methods
*Data Mining/methods
Metagenome
Biodiversity
RNA, Ribosomal, 16S/genetics
Ecosystem
Sequence Analysis, DNA

@article {pmid40594873,
year = {2025},
author = {Ahammad, AKS and Abid, MB and Ahmed, I and Mariom, and Khan, MGQ and Haque, MM and Wong, LL and Alam, MA and Bashar, MA},
title = {Transcriptomic profiling to unravel the underlying causes of early gonadal development of hilsa (Tenualosa ilisha) in Bangladesh.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22543},
pmid = {40594873},
issn = {2045-2322},
support = {5200//Bangladesh Fisheries Research Institute/ ; },
mesh = {Female ; *Gene Expression Profiling ; Bangladesh ; *Transcriptome ; Animals ; *Ovary/growth & development/metabolism ; Gene Expression Regulation, Developmental ; Gene Ontology ; },
abstract = {Hilsa (Tenualosa ilisha) is crucial to Bangladesh's economy and ecology, but recent trends show early maturation in small-sized hilsa, with unclear causes. This study aimed to identify differentially expressed genes (DEGs) between the ovaries of large and small hilsa using RNA-sequencing. Samples from both sizes were collected from the Meghna River in Chandpur District, and four ovary libraries were sequenced via the Illumina platform. A total of 908 DEGs were detected, of which 453 were up-regulated and 455 were down-regulated. Transcriptome analysis revealed significant differences in Gene Ontology terms such as extracellular region (GO:0005576), innate immune response (GO:0045087), and protein ubiquitination (GO:0016567), peptide antigen binding (GO:0042605), KEGG pathways including MAPK signaling pathway (ko04010), endocytosis (ko04144), and spliceosome (ko03040), as well as COG terms like signal transduction, between the ovary of large and small hilsa shad. These findings suggest that differentially expressed genes may play a role in regulating the ovarian development of T. ilisha. However, the entire process, from sampling to final annotation, is described here, along with the workflow. This study will offer a valuable resource for current and upcoming Hilsa transcriptome-based expression profiling studies.},
}

Female
*Gene Expression Profiling
Bangladesh
*Transcriptome
Animals
*Ovary/growth & development/metabolism
Gene Expression Regulation, Developmental
Gene Ontology

@article {pmid40594150,
year = {2025},
author = {Lin, Y and Zhou, J and Wang, J and Xu, H and Li, Y and Chen, F and Liu, Y},
title = {Spatiotemporal evolution and driving forces of landscape ecological risk in the lower reaches of the Yellow River from 2000 to 2020.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21375},
pmid = {40594150},
issn = {2045-2322},
support = {0031504//Shandong Top Talent Special Foundation/ ; 42201077//National Natural Science Foundation of China/ ; ZR2021QD074//Shandong Provincial Natural Science Foundation/ ; 2023M732105//China Postdoctoral Science Foundation/ ; SDMTKCY-2022-17//Open Subject of Institute of Coal Geology Planning Survey of Shandong Province/ ; 2024KJH087//the Youth Innovation Team Project of Higher School in Shandong Province, China/ ; },
mesh = {*Rivers ; China ; *Ecosystem ; Humans ; Spatio-Temporal Analysis ; *Conservation of Natural Resources ; Environmental Monitoring ; Human Activities ; Urbanization ; },
abstract = {Rapid urban development and human activities have led to drastic changes in land use, resulting to heightened ecological pressures and risks to ecosystems, especially in cities along the lower reaches of the Yellow River (CLRYR), China. However, the landscape pattern and associated ecological risks in the CLRYR in the past twenty years remain unclear. In this study, we employed the land use data to identify the primary landscape types and their transformations, providing an in-depth analysis of the prevailing landscape pattern and the landscape ecological risk (LER) in the CLRYR. Additionally, we explored the spatial distribution of LER and investigated the underlying driving forces behind these changes. The results reveal that: (1) Cropland is the main landscape type in the CLRYR region; however, the area of cropland decreases with the transition to impervious. (2) Due to human activities, landscape fragmentation and diversity have gradually increased in CLRYR, while aggregation has gradually decreased, until there was some improvement between 2015 and 2020. (3) The LER in the CLRYR region exhibits instability, with values of 0.1761, 0.1751, 0.1760, 0.1773, and 0.1751 displaying a fluctuating downward trend. Directional distribution analysis indicates a movement of the LER center of gravity towards the mouth of the Yellow River, accompanied by an increasing dispersion pattern. Analysis of driving forces suggests that natural factors hold greater explanatory power compared to social factors. Moreover, interaction detection results reveal that the combined effect of any two factors surpasses that of a single factor. The findings offer a theoretical foundation for enhancing planning policies aimed at striking a balance between environmental preservation and social advancement within the CLRYR region.},
}

*Rivers
China
*Ecosystem
Humans
Spatio-Temporal Analysis
*Conservation of Natural Resources
Environmental Monitoring
Human Activities
Urbanization

@article {pmid40593040,
year = {2025},
author = {Liu, S and Li, J and Xia, L and Li, R and Wang, J and Namkha, N},
title = {An integrated GIS-pXRF approach assesses ecological and human health risks from heavy metals in county level soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22834},
pmid = {40593040},
issn = {2045-2322},
support = {2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2024WHZ0237//Technology Innovation Center for Land Engineering and Human Settlements, Shaanxi Land Engineering Construction Group Co., Ltd and Xi'an Jiaotong University/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2023-CX-RKX-102//Innovation Capability Support Program of Shaanxi Province, China/ ; 2024WZ-YBXM-19//Shaanxi Province Foreign Expert Service Project/ ; 300102352502//Open Fund of Shaanxi Key Laboratory of Land Consolidation, China/ ; DJNY-YB-2023-20//Project of Shaanxi Province Land Engineering Construction Group/ ; DJNY-YB-2023-20//Project of Shaanxi Province Land Engineering Construction Group/ ; 2024JC-YBQN-0541//Natural Science Basic Research Program of Shaanxi Province/ ; },
mesh = {*Metals, Heavy/analysis ; Humans ; *Geographic Information Systems ; *Soil Pollutants/analysis ; China ; *Environmental Monitoring/methods ; *Soil/chemistry ; Risk Assessment ; Spectrometry, X-Ray Emission/methods ; },
abstract = {Counties in China are the primary components of small and mid-sized city (SMC), and at the core of China's future urbanization and industrialization development. Land is an essential nature resource providing the basis for urban-rural development, which is directly influenced by anthropogenic processes and in turn has impacts on human health. Clarifying the distribution characteristics and causes of heavy metals (HMs) pollution in soils is key to ensuring human health, as well as promoting land sustainability at county-level. In order to efficiently identify high risk regions of HMs pollution, this study proposed a geographic information system (GIS)-portable X-ray fluorescence (pXRF)-based approach to measure local soil background of HMs and to screen high risk regions in Shangzhou, China. ICP-MS and pXRF results showed a good agreement of Cr, Ni, Cu, Zn, Pb and As with R[2] ranging from 0.757 to 0.966. Soil background of Ni, Cu, Zn, As and Pb had increased by 33.34-129.74% compared to 1990 levels. HMs concentrations in soils of urban-rural fringe were generally larger than those of urban and rural area. Particularly, soil background of Zn and Pb in urban-rural fringe exceeded 28.90% and 19.93% of urban area, 46.33% and 41.91% of rural area, respectively. In high soil background regions, 25% of sampling points were considered as moderate risk or above, with ecological risk index (RI) greater than 150. As, Cr and Ni were identified as major contributors to human health risk, and children were more vulnerable than adults with considerably total non-carcinogenic risk (THI = 1.46) and carcinogenic health risk (TCR = 1.52 × 10[- 4]). Anthropogenic process including industrial manufacturing, agricultural practice, urban expansion and land conversion brought about the HMs accumulation in soils. This study indicated industrial zone in urban-rural fringe should be priority-controlled, and provided scientific basis for urban-rural environmental management and human health risk protection.},
}

*Metals, Heavy/analysis
Humans
*Geographic Information Systems
*Soil Pollutants/analysis
China
*Environmental Monitoring/methods
*Soil/chemistry
Risk Assessment
Spectrometry, X-Ray Emission/methods

@article {pmid40589590,
year = {2025},
author = {Richards, CS and Vera Cruz, D and Shapiro, JW and Wootton, JT and Pfister, CA},
title = {Spatially Varying Selection Amplifies Intrapopulation Differentiation Among Phenotypic Traits in the Rocky-Shore Mussel, Mytilus californianus.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71641},
pmid = {40589590},
issn = {2045-7758},
abstract = {Strong ecological gradients along heterogeneous environments play an important role in shaping population differentiation across species ranges. Thus, the selective pressure of environmental variation on phenotypic variation strongly affects an organism's ability to persist across diverse or new environments. We investigated the spatial variability of biological responses in the intertidal bivalve Mytilus californianus to highlight the costs and trade-offs of local adaptation and phenotypic plasticity across various functional traits in a dynamic environment, the marine intertidal. To test this, we performed a reciprocal transplant experiment with M. californianus individuals originating from the upper and lower intertidal measuring relevant phenotypic traits, followed by whole genome sequencing (WGS). We determined that morphological traits in individuals demonstrated phenotypic plasticity when moved to new environments, whereas physiological traits such as metabolism exhibited constraints in plasticity. Additionally, mussels from high intertidal zones, which experience greater heat and aerial exposure stress, maintained lower metabolic rates and showed increased frequencies of non-synonymous mutations in functionally relevant heat shock proteins when compared to low intertidal mussels. These results suggest that morphological and physiological traits responded differently to spatially varying selection within the marine intertidal.},
}

@article {pmid40588733,
year = {2025},
author = {Zhang, H and Fu, Y and Cao, C and Jiang, H and Tang, R and Dai, Z and Zhang, W},
title = {Identification and characterization of novel CRESS-DNA viruses in the human respiratory tract.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {211},
pmid = {40588733},
issn = {1743-422X},
support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801301 and 2022YFC2603801//National Key Research and Development Programs of China/ ; JLY2021151//Clinical Medicine Science and Technology Development Foundation of Jiangsu University/ ; },
mesh = {Humans ; Phylogeny ; *DNA Viruses/classification/genetics/isolation & purification ; Metagenomics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Respiratory System/virology ; Computational Biology ; *Nasopharynx/virology ; DNA, Viral/genetics ; Female ; Male ; Adult ; },
abstract = {CRESS-DNA viruses are small, circular, single-stranded DNA viruses that have been identified in diverse environments and hosts, including vertebrates, invertebrates, and environmental samples. However, their diversity and role in the human respiratory tract remain poorly understood. In this study, we employed viral metagenomics to analyze 140 nasopharyngeal swab samples from asymptomatic individuals. High-throughput sequencing and bioinformatics analyses were used to identify and characterize novel CRESS-DNA viruses. Phylogenetic relationships were inferred based on Rep protein sequences using maximum likelihood analysis. We identified and characterized eight novel CRESS-DNA viruses, which were classified into the families Endolinaviridae and Naryaviridae, with one potentially representing a novel viral family. These viruses exhibited typical circular genomic structures encoding Rep and Cap proteins, with conserved motifs associated with rolling circle replication. Phylogenetic analysis showed that some viruses were closely related to sequences from vertebrate hosts or environmental samples, suggesting a diverse ecological distribution. Our findings expand the known diversity of CRESS-DNA viruses in the human respiratory tract and highlight their potential ecological and evolutionary significance. Further studies are needed to explore their host specificity, replication mechanisms, and potential roles in human health and disease.},
}

Humans
Phylogeny
*DNA Viruses/classification/genetics/isolation & purification
Metagenomics
Genome, Viral
High-Throughput Nucleotide Sequencing
*Respiratory System/virology
Computational Biology
*Nasopharynx/virology
DNA, Viral/genetics
Female
Male
Adult

@article {pmid40588154,
year = {2025},
author = {Wang, Y and Li, H and Tan, F and Jin, LN and Su, J and Luo, C},
title = {Root and foliar uptake, bidirectional translocation, subcellular distribution, and metabolism of tire wear particle-derived p-phenylenediamines and their quinones in Chinese cabbage and bok choy.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126737},
doi = {10.1016/j.envpol.2025.126737},
pmid = {40588154},
issn = {1873-6424},
abstract = {Tire wear particles (TWPs) and TWP-derived compounds have caused global concern for their toxicity, but their impacts on vegetables, particularly through foliar absorption, remain largely unknown. We investigated the absorption, translocation, accumulation, and metabolism of TWP-derived p-phenylenediamines (PPDs) and PPD-quinones (PPDQs) in hydroponic and soil-cultured leafy vegetables by exposing them to TWPs through roots and leaves. PPDs and PPDQs can be absorbed by vegetables through both roots and leaves, with subsequent bidirectional translocation within vegetables. TWPs with smaller particle sizes and higher aging degrees can release more PPDs and PPDQs, resulting in increased absorptions by the vegetables. Leaves with higher wax secretion, lipid content, and trichome abundance exhibit greater uptake capabilities. PPDs and PPDQs absorbed by leaves can be released back into the environment through roots. The subcellular distribution and translocation of PPDs and PPDQs in vegetables are mainly controlled by their octanol-water partition coefficients with highly hydrophobic congeners primarily accumulating in cell walls and organelles. We screened the 6PPD and 6PPDQ metabolites in leafy vegetables and found that their metabolic processes are influenced by their exposure medium and tissue specificity. The results highlight the risks posed by vegetables absorbing, accumulating, and metabolizing airborne TWP-derived chemicals through their leaves.},
}

@article {pmid40425424,
year = {2025},
author = {Cardoso, P and Branco, V and Correia, L and Emerson, BC and Laine, VN and Lopes, M},
title = {Automated biodiversity research critically requires multidisciplinary expertise.},
journal = {Trends in ecology & evolution},
volume = {40},
number = {7},
pages = {626-628},
doi = {10.1016/j.tree.2025.05.003},
pmid = {40425424},
issn = {1872-8383},
mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; *Automation ; *Ecology/methods ; *Computational Biology/methods ; },
abstract = {Data-driven computational methods in taxonomy, ecology, and conservation biology are revolutionising these disciplines, from data collection to analysis and interpretation. However, effective automation requires both critical thinking about the limitations of the data and methods, and thorough training and validation by experts, supported by strong interdisciplinary collaboration.},
}

*Biodiversity
*Conservation of Natural Resources/methods
*Automation
*Ecology/methods
*Computational Biology/methods

@article {pmid40586834,
year = {2025},
author = {Moisa, MB and Roba, ZR and Purohit, S and Deribew, KT and Gemeda, DO},
title = {Evaluating the impact of land use and land cover change on soil moisture variability using GIS and remote sensing technology in southwestern Ethiopia.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {7},
pages = {824},
pmid = {40586834},
issn = {1573-2959},
mesh = {Ethiopia ; *Soil/chemistry ; *Remote Sensing Technology ; *Environmental Monitoring/methods ; Geographic Information Systems ; Agriculture ; Climate Change ; Conservation of Natural Resources ; Water/analysis ; Ecosystem ; Forests ; },
abstract = {Soil moisture dynamics are critical for agriculture, water resources, and climate resilience in Ethiopia, influencing crop yields, water availability, and ecosystem health. Assessing soil moisture variability in relation to land use and cover (LULC) changes is essential for effective ecosystem conservation and climate change adaptation, ensuring sustainable development and resilience to environmental challenges. This study examines the impact of LULC changes on soil moisture variability in Southwestern Ethiopia over 30 years (1994-2024). Utilizing Landsat Thematic Mapper (1994), Enhanced Thematic Mapper Plus (2004), and Operational Land Imager/Thermal Infrared Sensor (2024) data, LULC changes were analyzed using supervised classification approach with the Maximum Likelihood Algorithm. The classification process was conducted using ERDAS Imagine 2015 software. In addition, vegetation health and soil moisture dynamics were assessed through the Normalized Difference Vegetation Index (NDVI) and the Normalized Difference Moisture Index (NDMI). Results reveal a significant increase in cultivated land from 3595.2 km[2] (42.0%) to 6183.3 km[2] (72.2%), with a corresponding decrease in forest cover from 3119.2 km[2] (36.4%) to 2030.4 km[2] (23.7%).This significant shift indicates intensive agricultural expansion at the expense of forest cover, highlighting increased land conversion pressures. NDVI values dropped from 0.71 in 1994 to 0.52 in 2024, this decline in NDVI values signifies a substantial reduction in vegetation cover and density over the 30-year period. The NDMI results indicated a decrease in peak moisture levels and average soil moisture, emphasizing a growing trend of intensified dryness. This soil moisture decline is attributed to factors such as reduced precipitation, increased evaporation, and changes in LULC. The conversion of forest land to cultivation led to a significant decrease in NDMI values, reflecting a reduction in soil moisture due to the loss of forest cover and increased evapotranspiration from agricultural activities. A strong correlation (R[2] = 0.98) between NDVI and NDMI highlights that higher vegetation cover is associated with higher soil moisture. Therefore, the study highlights the profound impact of land use and land cover changes on soil moisture, underscoring the urgent need for sustainable land management practices. These practices are critical to combat environmental degradation, improve soil moisture retention, and bolster ecosystem resilience, ensuring a sustainable and climate-resilient future.},
}

Ethiopia
*Soil/chemistry
*Remote Sensing Technology
*Environmental Monitoring/methods
Geographic Information Systems
Agriculture
Climate Change
Conservation of Natural Resources
Water/analysis
Ecosystem
Forests

@article {pmid40585004,
year = {2025},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Uncertain moth, Hoplodrina octogenaria (Goeze, 1781).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {201},
pmid = {40585004},
issn = {2398-502X},
abstract = {We present a genome assembly from a male specimen of Hoplodrina octogenaria (Uncertain moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence has a total length of 476.65 megabases. Most of the assembly (99.98%) is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 15.93 kilobases.},
}

@article {pmid40578867,
year = {2025},
author = {Topalian, N and Fagherazzi, G and Perchoux, C},
title = {Daily mobility, activity and environmental determinants of stress in ecological momentary assessment (EMA) and GPS studies: a scoping review protocol.},
journal = {BMJ open},
volume = {15},
number = {6},
pages = {e091509},
pmid = {40578867},
issn = {2044-6055},
mesh = {Humans ; Scoping Review as Topic ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Stress, Psychological ; Research Design ; *Activities of Daily Living ; Environment ; },
abstract = {INTRODUCTION: Stress is omnipresent in our everyday lives and a key risk factor for our physical and mental health. Yet little is known about the impact of geographic life environments, linked to our daily activities and mobility patterns, on our momentary and daily stress levels.We propose this review to gather evidence on the spatio-temporal determinants of momentary or daily stress in studies using ecological momentary assessment (EMA) or experience sampling methods (ESM) in addition to global positioning systems (GPS) tracking. We will focus on the spatio-temporal definition and modelling of environmental exposures accounting for participant daily activities and mobility patterns and their association with stress.

METHODS AND ANALYSIS: This scoping review will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework for scoping reviews (2018). We will search the PubMed/Medline, Web of Science, PsycInfo and Scopus databases. We will include papers using EMA or ESM and GPS measuring chronic, daily or momentary stress as an outcome; these methods are also referred to as geographically-explicit ecological momentary assessment.Articles published from January 2000-June 2025 will be screened. Two independent reviewers will screen titles and abstracts to agree on the inclusion of articles. No geographical or population limitation will be imposed.

ETHICS AND DISSEMINATION: This study is a scoping review based on previously published and publicly available literature. It does not involve the collection of primary data, human participants, or the processing of personal or sensitive information. Therefore, ethical approval is not required in accordance with institutional and international research ethics guidelines. The results will be submitted in peer-reviewed journals and presented at international conferences.},
}

Humans
Scoping Review as Topic
*Ecological Momentary Assessment
*Geographic Information Systems
*Stress, Psychological
Research Design
*Activities of Daily Living
Environment

@article {pmid40578201,
year = {2025},
author = {Son, HF and Hwang, S and Kim, Y and Ahn, JH and Ko, JK and Gong, G and Um, Y and Park, JH and Park, HJ and Lee, SM},
title = {Enzymatic depolymerization of polyethylene using a small laccase and its potential for bio-upcycling.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139021},
doi = {10.1016/j.jhazmat.2025.139021},
pmid = {40578201},
issn = {1873-3336},
abstract = {Polyethylene (PE) plastics present significant environmental challenges due to their recalcitrant nature and widespread usage. This study explores the biological degradation of PE using a novel enzyme, small laccase from Amycolatopsis sp. ATCC 39116 (ASLAC). Among four selected laccases, ASLAC demonstrated the highest biomass production using PE as a carbon source when expressed by Yarrowia lipolytica. Surface analysis of PE films treated with purified ASLAC, using scanning electron microscopy (SEM) and atomic force microscopy (AFM), revealed substantial degradation of the material. The degradation products were successfully utilized by Y. lipolytica, underscoring its potential for converting PE into bioenergy. Structural analysis and molecular docking simulations revealed that the substrate binding site of ASLAC, characterized by a hydrophobic planner configuration, is highly optimized for binding and cleaving PE polymers. This unique structure distinguishes it from other laccases with narrower or obstructed binding sites. Phylogenetic analysis of 311 small laccase sequences classified ASLAC into the Type-Ia subgroup, which exhibited superior potential for PE degradation. This study establishes ASLAC as a promising biocatalyst for sustainable PE management, providing a foundation for future applications in bioremediation and polymer upcycling.},
}

@article {pmid40432231,
year = {2025},
author = {Tian, XC and Nie, S and Domingues, D and Rossi Paschoal, A and Jiang, LB and Mao, JF},
title = {PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.},
journal = {The New phytologist},
volume = {247},
number = {3},
pages = {1538-1549},
pmid = {40432231},
issn = {1469-8137},
support = {2022YFD2200103//National Key R&D Program of China/ ; 32171816//National Natural Science Foundation of China/ ; ZR2022YQ23//Natural Science Fund for Excellent Young Scholars of Shandong Province/ ; 2025A1515012969//Guangdong Basic and Applied Basic Research Foundation/ ; #440412/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico - CNPq/ ; Project: NAPI Bioinformatica #66.2021//Fundação Araucária/ ; },
mesh = {*RNA, Long Noncoding/genetics ; *RNA, Plant/genetics ; *Computational Biology/methods ; Algorithms ; *Plants/genetics ; RNA, Messenger/genetics ; *Software ; Open Reading Frames/genetics ; },
abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features - ORF coverage, complex Fourier average, and atomic Fourier amplitude - that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).},
}

*RNA, Long Noncoding/genetics
*RNA, Plant/genetics
*Computational Biology/methods
Algorithms
*Plants/genetics
RNA, Messenger/genetics
*Software
Open Reading Frames/genetics

@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
mesh = {*Metagenomics/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Computational Biology/methods ; DNA Barcoding, Taxonomic/methods ; Metagenome ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}

*Metagenomics/methods
*Biodiversity
*DNA, Environmental/genetics
*Computational Biology/methods
DNA Barcoding, Taxonomic/methods
Metagenome

@article {pmid40125978,
year = {2025},
author = {Bailey, N and Stevison, L and Samuk, K},
title = {Correcting for Bias in Estimates of θ w and Tajima's D From Missing Data in Next-Generation Sequencing.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14104},
pmid = {40125978},
issn = {1755-0998},
support = {R35GM147501/GM/NIGMS NIH HHS/United States ; R35GM147501/GM/NIGMS NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Genetics, Population/methods ; *Genetic Variation ; Software ; *Computational Biology/methods ; Bias ; },
abstract = {Population genetic analyses use information from the site frequency spectrum to infer evolutionary processes. Two summary statistics, Watterson's estimator (θ w) of genetic diversity, and Tajima's D , used for detecting non-neutral evolution, are among the most frequently computed statistics utilising this information. However, missing information in genomic data, particularly as encoded in the Variant Call Format (VCF), can bias these estimates, leading to incorrect evolutionary inferences. We assessed the impact of missing data on the estimation of these statistics using various population genetic software packages (VCFtools, PopGenome, pegas and scikit-allel). By simulating neutral genomic data with varying levels of missing genotypes and sites, we found consistent underestimation of θ w across programs. We found a consequent bias in estimates of Tajima's D , though the direction varied by software. We developed and implemented correction methods as functions in an update of the popular pixy software, significantly reducing these biases. Our findings highlight the need for accurate data handling in population genomics to avoid misinterpretations of evolutionary phenomena.},
}

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

@article {pmid40087979,
year = {2025},
author = {Van den Wyngaert, S and Cerbin, S and Garzoli, L and Grossart, HP and Gsell, AS and Kraberg, A and Lepère, C and Neuhauser, S and Stupar, M and Tarallo, A and Cunliffe, M and Gachon, C and Gavrilović, A and Masigol, H and Rasconi, S and Selmeczy, GB and Schmeller, DS and Scholz, B and Timoneda, N and Trbojević, I and Wilk-Woźniak, E and Reñé, A},
title = {ParAquaSeq, a Database of Ecologically Annotated rRNA Sequences Covering Zoosporic Parasites Infecting Aquatic Primary Producers in Natural and Industrial Systems.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14099},
pmid = {40087979},
issn = {1755-0998},
support = {PID2020-112978GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; CA20125//European Cooperation in Science and Technology/ ; 451-03-66/2024-03/200178//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 239548-051//RANNIS Icelandic Research Fund/ ; 340659//Research Council of Finland/ ; 346387//Research Council of Finland/ ; 101086521//European Commission/ ; IR0000005//European Commission/ ; NKFIH KKP 144068//National Laboratory for Water Science and Water Security/ ; RRF-2.3.1-21-2022-00008//National Laboratory for Water Science and Water Security/ ; Y0801-B16//Austrian Science Fund/ ; //AXA Research Fund/ ; ANR-21-BIRE-0002-01//Agence Nationale de la Recherche/ ; 101052342//Biodiversa+/ ; CIR-01_00028//Italian Ministry of University and Research/ ; GR1540/33-1//Deutsche Forschungsgemeinschaft/ ; GR1540/47-1//Deutsche Forschungsgemeinschaft/ ; GR1540/48-1//Deutsche Forschungsgemeinschaft/ ; GR1540/51-1//Deutsche Forschungsgemeinschaft/ ; CEX2019-000928-S//AEI/ ; },
mesh = {*Aquatic Organisms/parasitology ; *RNA, Ribosomal/genetics ; Microalgae/parasitology ; *Parasites/genetics/classification ; *Databases, Genetic ; },
abstract = {Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial-scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta-analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.},
}

*Aquatic Organisms/parasitology
*RNA, Ribosomal/genetics
Microalgae/parasitology
*Parasites/genetics/classification
*Databases, Genetic

@article {pmid40079420,
year = {2025},
author = {Jurburg, SD},
title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14102},
pmid = {40079420},
issn = {1755-0998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Metagenomics/methods ; Microbiota ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Metagenomics/methods
Microbiota
Animals
*DNA Barcoding, Taxonomic/methods
Biodiversity
Computational Biology/methods
Sequence Analysis, DNA/methods

@article {pmid40051336,
year = {2025},
author = {Birchard, K and Boccia, C and Lounder, H and Colston-Nepali, L and Friesen, VL},
title = {Popfinder: A Highly Effective Artificial Neural Network Package for Genetic Population Assignment.},
journal = {Molecular ecology resources},
volume = {25},
number = {6},
pages = {e14096},
pmid = {40051336},
issn = {1755-0998},
support = {//Environment and Climate Change Canada/ ; },
mesh = {*Neural Networks, Computer ; Animals ; *Genetics, Population/methods ; *Computational Biology/methods ; *Software ; *Birds/genetics/classification ; },
abstract = {The ability to assign biological samples to source populations with high accuracy and precision based on genetic variation is important for numerous applications from ecological studies through wildlife conservation to epidemiology. However, population assignment when genetic differentiation is low is challenging, and methods to address this problem are lacking. The application of artificial neural networks to population assignment using genomic data is highly promising. Here we present popfinder: a new, easy-to-use Python-based artificial neural network pipeline for genetic population assignment. We tested popfinder both with simulated genetic data from populations connected by varying levels of gene flow and with reduced-representation sequence data for three species of seabirds with weak to no population genetic structure. Popfinder was able to assign individuals to their source populations with high accuracy, precision and recall in most cases, including both simulated and empirical data sets, except in the empirical data set with the weakest population structure, where the comparator programs also performed poorly. Compared to other available software, popfinder was slower on the simulated data sets due to hyperparameter tuning and the fact that it does not reduce the dimensionality of the data set; however, all programs ran in seconds on empirical data sets. Additionally, popfinder provides a perturbation ranking method to help develop optimised SNP panels for genetic population assignment and is designed to be user-friendly. Finally, we caution users of all assignment programs to watch both for leakage of data during model training, which can lead to overfitting and inflation of performance metrics, and for unequal detection probabilities.},
}

*Neural Networks, Computer
Animals
*Genetics, Population/methods
*Computational Biology/methods
*Software
*Birds/genetics/classification

@article {pmid40577234,
year = {2025},
author = {Roberts, T and Hanan, NP},
title = {Sapflow Database Reveals Density-Dependent Competition Among Woody Plants at Global Scale.},
journal = {Ecology letters},
volume = {28},
number = {6},
pages = {e70167},
pmid = {40577234},
issn = {1461-0248},
support = {DEB 2025166//National Science Foundation/ ; //New Mexico Space Consortium/ ; },
mesh = {Databases, Factual ; *Water/metabolism ; Ecosystem ; *Trees/physiology ; },
abstract = {Though limiting resources differ among systems, water is limiting in most arid and many mesic systems, potentially allowing for direct measurement of competition by measurement of water uptake. Sapflow measurements provide a direct measure of water movement through plant stems, but, to our knowledge, sapflow has never been used to study density dependence and competition at large (regional or global) scales. Here, we examine a global database of sapflow measurements, the SapFluxNet database, for signs of density-dependent competition for water. We find that plant-level water uptake decreases with increasing competition from neighbours (specifically, neighbourhood basal area). Further analysis demonstrates that global-scale variability in annual sapflow can be largely explained (R[2] = 0.522) by the combination of average vapour pressure and neighbourhood summed basal area. This analysis provides a rare quantification of plant competition for a limiting resource inferred directly via measurements of resource acquisition (i.e., sapflow).},
}

Databases, Factual
*Water/metabolism
Ecosystem
*Trees/physiology

@article {pmid40573089,
year = {2025},
author = {Suarez, C and Adibi, S},
title = {Integrating Traditional Nutritional Wisdom into Digital Nutrition Platforms: Toward Culturally Adaptive and Inclusive Health Technologies.},
journal = {Nutrients},
volume = {17},
number = {12},
pages = {},
pmid = {40573089},
issn = {2072-6643},
mesh = {Humans ; *Biomedical Technology/methods ; Culture ; *Digital Technology ; Health Knowledge, Attitudes, Practice ; *Nutritional Sciences ; },
abstract = {Background/Objectives: Traditional nutritional knowledge, shaped by centuries of cultural and ecological adaptation, offers holistic and sustainable dietary frameworks that remain highly relevant to modern health challenges. However, current digital nutrition platforms often fail to reflect this diversity, relying instead on standardized models with limited cultural sensitivity. This paper aims to explore how traditional nutritional wisdom can be integrated into digital health platforms to promote more inclusive and effective approaches to personalized nutrition. Methods: This perspective paper employs a cultural adaptation framework to analyze the integration of traditional food knowledge into digital contexts. Drawing from interdisciplinary research across nutrition science, anthropology, digital health and implementation science, we utilize the Knowledge-to-Action (KTA) Framework and the PEN-3 Cultural Model to structure our analysis. A systematic scoping review of literature published between 2010 and 2025 was conducted to identify integration challenges and opportunities. Additionally, we analyzed case studies of three traditional dietary systems (Argentina, Italy and Japan) and evaluated five leading digital nutrition platforms for their degree of cultural inclusivity, using qualitative comparative methods. Results: The analysis highlights significant challenges in adapting traditional knowledge to digital formats, including standardization barriers, contextual loss and technological limitations. However, successful integration initiatives demonstrate that through participatory design, flexible data architectures and culturally-informed algorithms, traditional food systems can be meaningfully represented. Our proposed four-phase integration framework-documentation, digital adaptation, implementation and evaluation-provides a structured approach for developers and researchers. Conclusions: Bridging traditional nutrition with digital platforms represents a vital opportunity to enhance personalization and preserve food heritage while improving health outcomes for diverse populations. This integration requires interdisciplinary collaboration, user-centered design processes and ethical approaches that respect cultural ownership and context.},
}

Humans
*Biomedical Technology/methods
Culture
*Digital Technology
Health Knowledge, Attitudes, Practice
*Nutritional Sciences

@article {pmid40571921,
year = {2025},
author = {Demsash, AW and Abebe, R and Gezimu, W and Kitil, GW and Tizazu, MA and Lambebo, A and Bekele, F and Alemu, SS and Jarso, MH and Dube, GN and Wedajo, LF and Purohit, S and Kalayou, MH},
title = {Correction: Data-driven machine learning algorithm model for pneumonia prediction and determinant factor stratification among children aged 6-23 months in Ethiopia.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {808},
pmid = {40571921},
issn = {1471-2334},
}

@article {pmid40562960,
year = {2025},
author = {Habibie, MI and Hariyanto, and Arifandri, R and Qonita, Z and Kricella, P and Khoirudin, MH and Fuadi, NMR and Shabrina, N and Gutami, NI and Sadiah, S and Kartikasari, D and Widodo, MMA and Waluyo, and Binaruno, FA and Ismoyo, K},
title = {A comparative study of fully automatic and semi-automatic methods for oil spill detection using Sentinel-1 data.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {7},
pages = {808},
pmid = {40562960},
issn = {1573-2959},
mesh = {*Petroleum Pollution/analysis/statistics & numerical data ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; Machine Learning ; Indonesia ; Geographic Information Systems ; Neural Networks, Computer ; },
abstract = {The oil spill detection and assessment study conducted in the Banten Province of Indonesia involves the application of Sentinel-1 satellite data and machine learning tools in the year 2024. Synthetic Aperture Radar (SAR) data were used with VV polarization to observe the surface characteristics, using an oil spill threshold of - 25 dB to differentiate clean water from the oil spill based on low backscatter intensity. After desiring image processing and binary masking applications on the data that improve visibility of the oil spill-affected zones, vectorization was conducted for integration into geographic information systems (GIS). A temporal analysis indicated high variability across the spill sizes with an extreme peak on May 16 (79.686 km[2]) and July 3 (41.593 km[2]), which are likely dictated by the weather and oceanographic conditions plus the ship traffic of that time. Wind pattern analysis via ERA5 reanalysis data presented more insight into spill dispersion dynamics. Three machine learning classifiers were applied toward oil spill detection, namely Artificial Neural Networks (ANN), Random Forest (RF), and Extreme Gradient Boosting (XGBoost). Performance metrics indicate the ANN outperformed in discriminative ability (AUC = 0.92), while RF was highly accurate (99.01%) and precise (99.02%). This clearly demonstrates the viability of using an integrated approach of remote sensing, advanced image processing, and supervised learning for environmental monitoring and provides important information for minimizing ecological impacts and optimizing disaster response plans for maritime areas. Such an integrated scheme calls for advanced technology to combat ecological threats in maritime areas and provides crucial evidence toward ongoing interventions to protect and manage marine ecosystems and the associated local communities.},
}

*Petroleum Pollution/analysis/statistics & numerical data
*Environmental Monitoring/methods
*Water Pollutants, Chemical/analysis
Machine Learning
Indonesia
Geographic Information Systems
Neural Networks, Computer

@article {pmid40561147,
year = {2025},
author = {Impalli, I and Bergland, E and Saad-Roy, CM and Grenfell, BT and Levin, SA and Larsson, DGJ and Laxminarayan, R},
title = {Optimal sampling frequency and site selection for wastewater and environmental surveillance of infectious pathogens: A value of information assessment.},
journal = {PLoS computational biology},
volume = {21},
number = {6},
pages = {e1013190},
pmid = {40561147},
issn = {1553-7358},
mesh = {Humans ; *Wastewater/microbiology ; *Environmental Monitoring/methods ; Animals ; Computational Biology ; *Communicable Diseases/epidemiology ; Computer Simulation ; Disease Outbreaks ; Sensitivity and Specificity ; },
abstract = {Wastewater and environmental surveillance (WES) is a promising method of detecting infectious diseases in human and animal populations and offers significant advantages over traditional surveillance methods in the early detection of outbreaks. However, WES involves financial and human resources, and public policy decisions must determine whether the benefits of WES outweigh the costs, particularly in low-resource areas. The selection of surveillance sites, sampling frequency, and test sensitivity and specificity are crucial determinants of WES effectiveness and cost-efficiency. We created an analytical model and numerical simulations of disease arrival, spread, and WES strategies to determine the optimal sampling frequency for two interacting patches, each represented by a different sampling site. We show that it is optimal to test in one patch more frequently than it is to test in both patches less frequently if the patches are sufficiently interactive, surveillance is of sufficient sensitivity and specificity, and setup costs are substantial. In our value of information (VOI) assessment, the net value of surveillance information for both patches is non-monotonic with respect to the degree of patch interaction. Increased mixing between the patches allows for quicker surveillance detection but is worse for overall infection burden. Overall, optimizing the value of surveillance information for all patches being surveilled requires coordination and deliberate selection of surveillance sites and sampling frequencies. This paper provides a VOI assessment of WES to determine the optimal number of sites and sampling frequency at a high level of abstraction, leaving opportunity to adapt the model to specific pathogens and populations as needed. Our findings can inform the cost-efficient implementation of WES for infectious diseases, particularly in resource-constrained settings.},
}

Humans
*Wastewater/microbiology
*Environmental Monitoring/methods
Animals
Computational Biology
*Communicable Diseases/epidemiology
Computer Simulation
Disease Outbreaks
Sensitivity and Specificity

@article {pmid40561027,
year = {2025},
author = {Otte, A and Wohlrab, S and Moritz, F and Müller, C and Janouškovec, J and Michálek, J and Cembella, A and Voss, D and Wang, X and Tebben, J and Larsen, TO and Edvardsen, B and Schmitt-Kopplin, P and John, U},
title = {High-resolution multiomics links nutrients and mixotrophy to toxicity in a harmful bloom of the haptophyte Chrysochromulina leadbeateri.},
journal = {Science advances},
volume = {11},
number = {26},
pages = {eadv3390},
pmid = {40561027},
issn = {2375-2548},
mesh = {*Harmful Algal Bloom ; *Haptophyta/metabolism/genetics/growth & development ; *Nutrients/metabolism ; Polyketide Synthases/metabolism/genetics ; Multiomics ; },
abstract = {Harmful algal blooms (HABs) of the toxigenic haptophyte Chrysochromulina are known to cause fish mortalities and collateral ecosystem damage. The ichthyotoxic mechanisms are poorly understood but likely dependent on toxigenesis by polyketide synthases (PKSs). We hypothesize that induction of PKS activity facilitates mixotrophic behavior during nutrient-depleted bloom conditions. To identify potential in situ stimuli for growth, toxigenicity, and bloom persistence, we compared environmental factors and biological processes identified by metaomics to Chrysochromulina leadbeateri HABs between two fjords in northern Norway. We identified the polyketide ichthyotoxin leadbeaterin-1 from the C. leadbeateri bloom and found potentially associated candidate PKS genes of which most were higher expressed at bloom stations. A relative depletion of inorganic nitrogen and phosphate during the bloom was correlated with higher expression of genes involved in endocytosis, autophagy, and lysosomal activity. Mixotrophy is evidently a compensatory nutritional strategy coupled to induction of toxigenesis and other metabolomic processes as biotic factors linked to Chrysochromulina bloom dynamics.},
}

*Harmful Algal Bloom
*Haptophyta/metabolism/genetics/growth & development
*Nutrients/metabolism
Polyketide Synthases/metabolism/genetics
Multiomics

@article {pmid40299786,
year = {2025},
author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Prasanna, P and Chen, C and Damaghi, M},
title = {Eco-Evolutionary Guided Pathomic Analysis Detects Biomarkers to Predict Ductal Carcinoma In Situ Upstaging.},
journal = {Cancer research},
volume = {85},
number = {13},
pages = {2537-2547},
doi = {10.1158/0008-5472.CAN-24-2070},
pmid = {40299786},
issn = {1538-7445},
support = {U01CA261841//National Institutes of Health (NIH)/ ; R01CA272601//National Institutes of Health (NIH)/ ; R01CA249016//National Institutes of Health (NIH)/ ; R01CA297843//National Institutes of Health (NIH)/ ; R21CA258493-02S1//National Institutes of Health (NIH)/ ; R01GM148970//National Institute of General Medical Sciences (NIGMS)/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/pathology/metabolism/diagnosis/genetics ; *Biomarkers, Tumor/metabolism/analysis ; *Carcinoma, Intraductal, Noninfiltrating/pathology/metabolism/diagnosis/genetics ; Tumor Microenvironment ; Retrospective Studies ; Neoplasm Staging ; Disease Progression ; Middle Aged ; Prognosis ; },
abstract = {UNLABELLED: Cancers evolve in a dynamic ecosystem. Thus, characterizing the ecological dynamics of cancer is crucial to understanding cancer evolution, which can lead to the discovery of biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts, and biomarkers are needed to predict which cases will progress to aggressive disease. In this study, we showed that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. Quantitative analyses were performed on immunohistologic images from a retrospective cohort of DCIS specimens collected from biopsy samples. First, an eco-evolutionary designed approach was developed to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, cancer cells with metabolic phenotypes attributed to their habitats were identified, including a hypoxia-responding CA9+ phenotype and an acid-adapted LAMP2b+ phenotype. Whereas these markers have traditionally shown limited, if any, predictive capabilities for DCIS progression when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Additionally, the distribution of distinct niches with specific spatial patterns of these biomarkers predicted patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. A random forest classifier that was trained and underwent a five-fold validation on the biopsy cohort achieved an AUC of 0.74 for predicting clinical outcome. These results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for biomarker discovery.

SIGNIFICANCE: Evolutionary dynamics of the various niches composing the tumor ecosystem can be harnessed for predicting cancer progression, demonstrating how eco-evolutionary-designed approaches can guide biomarkers discovery studies in the era of digital pathology. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI.},
}

Humans
Female
*Breast Neoplasms/pathology/metabolism/diagnosis/genetics
*Biomarkers, Tumor/metabolism/analysis
*Carcinoma, Intraductal, Noninfiltrating/pathology/metabolism/diagnosis/genetics
Tumor Microenvironment
Retrospective Studies
Neoplasm Staging
Disease Progression
Middle Aged
Prognosis

@article {pmid39810621,
year = {2025},
author = {Gottlieb, E and Gupta, S and Gahan, L and Raymann, RJ and Watson, NF},
title = {Social jetlag decreases across the lifespan: A prospective big data analysis of objective sleep metrics.},
journal = {Journal of sleep research},
volume = {34},
number = {4},
pages = {e14433},
doi = {10.1111/jsr.14433},
pmid = {39810621},
issn = {1365-2869},
mesh = {Humans ; Female ; Male ; Middle Aged ; *Jet Lag Syndrome/physiopathology ; Adult ; *Sleep/physiology ; Prospective Studies ; Big Data ; Polysomnography ; Aged ; Longitudinal Studies ; Self Report ; Retirement ; Caffeine ; Age Factors ; Circadian Rhythm/physiology ; Cross-Sectional Studies ; },
abstract = {Changes in social zeitgebers across the lifespan affect the interaction between biological and social clocks, potentially contributing to social jetlag. Extant literature suggests a reduction in social jetlag given declining social obligations occurring after retirement, but is limited to self-reported methods and cross-sectional designs. Leveraging longitudinal and ecologically valid data from consumer sleep technology, we analysed objective sleep data from 2439 users of the polysomnography-validated SleepScore mobile application, encompassing 500,415 total nights recorded. We examined the relationship between age as a continuous variable, age as a proxy for retirement status, and social jetlag. Additional linear models were employed to assess the effect of self-reported chronotype, average reported daily caffeine, alcohol and stress on social jetlag. There was a significant negative association between overall age and social jetlag (β = -0.64, t = -9.90, p < 0.001, effect size = 0.040), such that every 1-year increase in age corresponded with a 0.64-min reduction in social jetlag. The inclusion of self-reported chronotype, stress, caffeine and alcohol increased the explanatory power of our models slightly, but the effect of age remained consistent (β = -0.642, t = -8.91, p < 0.001, effect size = 0.046). Retirement-aged individuals exhibited nearly 50% less reduction in social jetlag than pre-retirement (30.6 ± 48.2 min versus post-retirement: 15.8 ± 41.6 min, p < 0.0001). While social jetlag after retirement was most pronounced for strong evening chronotypes (β = -0.41, t = -2.876, p = 0.004, effect size = -0.4276), pairwise comparisons revealed no statistically significant differences in the slopes between chronotypes (p > 0.05). Thus, social jetlag decreases across the lifespan, and its reduction appears to be amplified post-retirement even after accounting for behavioural factors.},
}

Humans
Female
Male
Middle Aged
*Jet Lag Syndrome/physiopathology
Adult
*Sleep/physiology
Prospective Studies
Big Data
Polysomnography
Aged
Longitudinal Studies
Self Report
Retirement
Caffeine
Age Factors
Circadian Rhythm/physiology
Cross-Sectional Studies

@article {pmid40559311,
year = {2025},
author = {Liang, X and Yu, S and Meng, B and Ju, Y and Wang, S and Wang, Y},
title = {Machine-Learning-Guided Design of Nanostructured Metal Oxide Photoanodes for Photoelectrochemical Water Splitting: From Material Discovery to Performance Optimization.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {40559311},
issn = {2079-4991},
support = {LH2022B019//Heilongjiang Provincial Natural Science Foundation of China/ ; },
abstract = {The rational design of photoanode materials is pivotal for advancing photoelectrochemical (PEC) water splitting toward sustainable hydrogen production. This review highlights recent progress in the machine learning (ML)-assisted development of nanostructured metal oxide photoanodes, focusing on bridging materials discovery and device-level performance optimization. We first delineate the fundamental physicochemical criteria for efficient photoanodes, including suitable band alignment, visible-light absorption, charge carrier mobility, and electrochemical stability. Conventional strategies such as nanostructuring, elemental doping, and surface/interface engineering are critically evaluated. We then discuss the integration of ML techniques-ranging from high-throughput density functional theory (DFT)-based screening to experimental data-driven modeling-for accelerating the identification of promising oxides (e.g., BiVO4, Fe2O3, WO3) and optimizing key parameters such as dopant selection, morphology, and catalyst interfaces. Particular attention is given to surrogate modeling, Bayesian optimization, convolutional neural networks, and explainable AI approaches that enable closed-loop synthesis-experiment-ML frameworks. ML-assisted performance prediction and tandem device design are also addressed. Finally, current challenges in data standardization, model generalizability, and experimental validation are outlined, and future perspectives are proposed for integrating ML with automated platforms and physics-informed modeling to facilitate scalable PEC material development for clean energy applications.},
}

@article {pmid40558602,
year = {2025},
author = {Mpuhua, CAM and Souza, OF and Daboin, BEG and Bezerra, IMP and Na Blei, M and Sarti, TD and Silva, VEBD and Abreu, LC},
title = {Proportional Stroke Mortality in Espírito Santo, Brazil: A 20-Year Joinpoint Regression Study.},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {6},
number = {2},
pages = {},
pmid = {40558602},
issn = {2673-3986},
support = {001/2025//Fapes. Fundação de Amparo à Pesquisa do Estado do Espírito Santo, Brazil./ ; },
abstract = {Introduction: Stroke is one of the leading causes of death and disability worldwide. In Brazil, it remains the primary cause of mortality among adults. Although overall stroke mortality rates have declined, the absolute number of stroke incidents, deaths, and years of life loss continues to rise, particularly in developing and underdeveloped countries. Objective: The aim of this study was to analyze trends in stroke mortality across different age groups and both sexes in Espírito Santo, Brazil, from 2000 to 2021. Methods: This ecological time series study utilized secondary data from Espírito Santo, Brazil, from 2000 to 2021. Mortality data, categorized by sex and age group, were obtained from the Department of Informatics of the Unified Health System (DATASUS) database. Stroke-related mortality included deaths recorded under the International Classification of Diseases, 10th Revision (ICD-10) codes for subarachnoid hemorrhage (I60), intracerebral hemorrhage (I61), cerebral infarction (I63), and stroke not specified as hemorrhagic or ischemic (I64). Temporal trends in stroke mortality were assessed using joinpoint regression analysis. Results: From 2000 to 2021, there was a significant reduction in proportional mortality from stroke, with an overall decrease of -3.7% (p < 0.001). When analyzed by sex, the decline was -3.0% (p < 0.001) for males and -3.9% (p < 0.001) for females. The most significant decrease in proportional mortality was observed in the 50 to 59 age group, with an average annual percentage change of -4.9% (p < 0.001). The 30 to 39 age group exhibited the smallest decline, with an average annual percentage change of -2.4% (p < 0.001). No significant segments were observed in the 40 to 49, 60 to 69, and 70 to 79 age groups during the study period. Conclusions: This study identified a notable decline in stroke-related proportional mortality in the adult population of Espírito Santo between 2000 and 2021. While males had a higher absolute number of deaths, females exhibited a higher proportional mortality rate, underscoring the need for targeted preventive measures and effective acute stroke treatment, particularly among men.},
}

@article {pmid40556364,
year = {2025},
author = {Peat, GM and Hill, JC and Yu, D and Wathall, S and Parry, E and Bailey, J and Stevenson, K and Thompson, C and Wilkie, R and Dziedzic, K and Jordan, KP and , },
title = {Local variation in musculoskeletal pain consultation rates in primary care: findings from an ecologic study in Staffordshire.},
journal = {Primary health care research & development},
volume = {26},
number = {},
pages = {e52},
pmid = {40556364},
issn = {1477-1128},
mesh = {Humans ; *Musculoskeletal Pain/epidemiology/therapy ; Male ; Female ; *Primary Health Care/statistics & numerical data ; Middle Aged ; Adult ; England/epidemiology ; *Referral and Consultation/statistics & numerical data ; Aged ; Prevalence ; Chronic Pain/epidemiology ; Self Report ; Young Adult ; Adolescent ; },
abstract = {Variation between general practices in the rate of consultations for musculoskeletal pain conditions may signal important differences in access to primary care, perceived usefulness, or available alternative sources of care; however, it might also just reflect differences in underlying 'need' between practices' registered populations. In a study of 30 general practices in Staffordshire, we calculated the proportion of adults consulting for a musculoskeletal pain condition, then examined this in relation to selected practice and population characteristics, including the estimated prevalence of self-reported musculoskeletal problems and chronic pain in each practices' registered population. Between September 2021 and July 2022, 18,388 adults were consulted for a musculoskeletal pain condition. After controlling for length of recruitment, time of year, and age-sex structure, the proportion consulting varied up to two-fold between practices but was not strongly associated with the prevalence of self-reported long-term musculoskeletal problems, chronic pain, and high-impact chronic pain.},
}

Humans
*Musculoskeletal Pain/epidemiology/therapy
Male
Female
*Primary Health Care/statistics & numerical data
Middle Aged
Adult
England/epidemiology
*Referral and Consultation/statistics & numerical data
Aged
Prevalence
Chronic Pain/epidemiology
Self Report
Young Adult
Adolescent