@article {pmid41839346,
year = {2026},
author = {Plaza, MP and Oteros, J and Leier-Wirtz, V and Charalampopoulos, A and Galán, C and Holzmann, C and Kolek, F and Vokou, D and Traidl-Hoffmann, C and Gilles, S and Damialis, A},
title = {An ensemble-forecasting model for airborne grass pollen at three climatically distinct sites.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124273},
doi = {10.1016/j.envres.2026.124273},
pmid = {41839346},
issn = {1096-0953},
abstract = {Precise airborne pollen forecasting is essential for mitigating exposure risks in individuals with pollen-related respiratory diseases such as allergic rhinitis and asthma, and for supporting timely public health warning. . While long-term accurate pollen forecasts could also support biodiversity conservation, ecosystem functions, and public-health protection. We developed an ensemble forecasting model for airborne grass (Poaceae) pollen concentrations in three climatically distinct European cities: Augsburg (Germany, transitional temperate-continental), Córdoba (Spain, dry Mediterranean), and Thessaloniki (Greece, humid Mediterranean). Pollen data (2018-2024) from Hirst-type volumetric traps were combined with meteorological parameters (temperature, humidity, precipitation). The 2024 pollen data were used for validation. Of 61 candidates, seven representative model families (Regularized Linear Regression, Extreme Gradient Boosting, Neural Network Autoregression [NNETAR], Random Rorest, Support Vector Regression, Prophet-XGBoost hybrid, and Autoregressive Integrated Moving Average [ARIMA]) were selected for the ensemble. Model weights were assigned according to predictive performance. The ensemble achieved R[2] values of 0.66 in Augsburg, 0.62 in Córdoba and 0.84 in Thessaloniki, with NNETARand/or ARIMA contributing most strongly during the pollen season. Lagged pollen concentrations and previous-day temperature emerged as key predictors. When incorporating data from an automatic pollen monitor (BAA500, Helmut Hund GmbH) in Augsburg, the model achieved higher predictive performance (R[2] = 0.89). Our findings demonstrate that ensemble-based pollen forecasting can generalize across contrasting bioclimatic regions while remaining sensitive to local ecological and climatic controls. This framework provides a foundation for more powerful (real-time) forecasting systems aimed primarily at improving daily allergy risk management, while potentially offering complementary insights into longer-term vegetation dynamics under climate variability.},
}

@article {pmid41840729,
year = {2026},
author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T},
title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02385-x},
pmid = {41840729},
issn = {2049-2618},
support = {JPMJND2206//Japan Science and Technology Agency/ ; },
abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.

RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.},
}

@article {pmid41840917,
year = {2026},
author = {Dwivedi, N and Heighton, SP and Laso-Jadart, R and Verry, AJF and Nieto-Heredia, A and Lesturgie, P and Khost, DE and Bohec, M and Sackton, TB and Chikhi, L and Orlando, L and Hume, JP and Achaz, G and Thèves, C and Mona, S and Warren, BH},
title = {Combining Population Genomics With Ancient DNA to Understand Island Colonisation History of the Madagascar Turtle Dove.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70299},
doi = {10.1111/mec.70299},
pmid = {41840917},
issn = {1365-294X},
support = {ANR-20-CE02-0009//Agence Nationale de la Recherche/ ; ANR-10-EQPX-03//Agence Nationale de la Recherche/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche/ ; INCa-DGOS-465//Institut Curie/ ; INCa-DGOS-Inserm_12554//Institut Curie/ ; },
mesh = {Animals ; *Genetics, Population ; *DNA, Ancient/analysis ; Islands ; Madagascar ; Population Density ; Mauritius ; Genetic Variation ; Genomics ; Humans ; },
abstract = {The Mascarene archipelago (Mauritius, Reunion and Rodrigues), characterised by first human arrival being recent, offers a unique setting to study species colonisation on a recent timescale, and contribution of past human interventions. Here we use a combination of modern and ancient DNA data as a case study to investigate the colonisation history of a species of concern in relation to conservation programmes-the Madagascar turtle dove (Nesoenas picturata) on Mauritius and Reunion. We generated a reference genome and re-sequenced genomes from contemporary N. picturata populations, as well as genome-wide data from relevant subfossils. A combination of model-free inferences, site frequency spectrum (SFS) based demographic modelling, and analyses of population structure including that of subfossils indicate that N. picturata colonised both islands independently and naturally from Madagascar, long before human arrival. Summary statistics and SFS-based modelling reveal large effective population sizes (Ne) and high genetic diversity in island populations, conflicting with historical accounts of human-induced demographic collapse. Based on goodness-of-fit, genetic structure and diversity indices do not discriminate between two best-fitting models, one of which posits large recent Ne and negligible translocation rates, while the other supports recent severe bottlenecks followed by high post-human translocation from Madagascar. Nonetheless, linkage disequilibrium provides stronger evidence for the latter scenario, which may also explain high genetic diversity. Both modern and ancient DNA data sources independently support the classification of N. picturata as native to both islands. Our findings highlight the potential of resolving colonisation history on timescales that have often been too recent for resolution, using a combination of different data sources, and by validating demographic models with multiple summary statistics.},
}

Animals
*Genetics, Population
*DNA, Ancient/analysis
Islands
Madagascar
Population Density
Mauritius
Genetic Variation
Genomics
Humans

@article {pmid41833453,
year = {2026},
author = {Gambetta Vianna, J and Benedetti, B and Di Carro, M and Magi, E},
title = {Emerging Contaminants in Raw and Cooked Marine Mussels: The QuEChERS Approach Combined With High-Performance Liquid Chromatography Coupled With Tandem Mass Spectrometry.},
journal = {Journal of mass spectrometry : JMS},
volume = {61},
number = {4},
pages = {e70047},
doi = {10.1002/jms.70047},
pmid = {41833453},
issn = {1096-9888},
mesh = {Tandem Mass Spectrometry/methods ; Animals ; Chromatography, High Pressure Liquid/methods ; *Mytilus/chemistry ; *Food Contamination/analysis ; Cooking ; *Bivalvia/chemistry ; *Water Pollutants, Chemical/analysis ; *Seafood/analysis ; },
abstract = {Mussel aquaculture has experienced substantial growth in recent decades, with global production exceeding 2.17 megatons (live weight), more than doubling since the early 21st century. Representing nearly 94% of the total mussel production, aquaculture plays a crucial economic and ecological role. Mussels accumulate xenobiotics through their filter-feeding behaviour, providing valuable insights into potential human exposure to the contaminants. However, the high lipid and protein content in their tissue can introduce analytical challenges, requiring rigorous clean-up procedures to mitigate matrix effects. Herein, we applied a QuEChERS-based extraction method coupled with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to investigate the occurrence of emerging contaminants (ECs) in raw and boiled Mytilus galloprovincialis samples. Samples were collected from three aquaculture farms supplying mussels to fish markets in Liguria (Italy), aiming to provide a representative overview of contamination across different geographical sources. A total of 36 samples were analysed, detecting ECs in 26 samples. Caffeine was the most frequently detected contaminant, consistent with its widespread consumption. Additionally, UV filters were also commonly found in the samples, likely due to the sampling period at the end of summer, when sunscreen use is highest. This is the first study to investigate the impact of cooking on the concentrations of different classes of ECs in mussels, reflecting real consumption conditions. Box and whisker plots revealed consistently higher contaminant concentrations in boiled samples, suggesting that thermal processing may influence contaminant release. This study aims to offer insights into contaminants distribution and preliminary information for human exposure assessment of potential risks to human health.},
}

Tandem Mass Spectrometry/methods
Animals
Chromatography, High Pressure Liquid/methods
*Mytilus/chemistry
*Food Contamination/analysis
Cooking
*Bivalvia/chemistry
*Water Pollutants, Chemical/analysis
*Seafood/analysis

@article {pmid41835092,
year = {2026},
author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {130},
pmid = {41835092},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.},
}

@article {pmid41836070,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Green, Dryobotodes eremita (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {208},
doi = {10.12688/wellcomeopenres.19300.2},
pmid = {41836070},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Dryobotodes eremita (the Brindled Green; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 709.8 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,706 protein coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41836754,
year = {2025},
author = {Gan, G and Chen, R and Zheng, P and Long, K and Cheng, KKY and Sulaiman, JE and Huang, X},
title = {Oral pathogens meet the gut microbiome: new mechanistic insights on systemic disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1673512},
doi = {10.3389/fcimb.2025.1673512},
pmid = {41836754},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Mouth/microbiology ; Inflammation/microbiology ; Probiotics ; Animals ; Fusobacterium nucleatum/pathogenicity ; },
abstract = {The oral-gut axis represents a critical bidirectional pathway linking oral microbiota to systemic health. Dysbiosis of the oral microbiome, driven by pathogens like Porphyromonas gingivalis, Fusobacterium nucleatum, Streptococcus species, and Helicobacter pylori, disrupts gut ecology via direct translocation, metabolite signaling (e.g., TMAO, SCFAs), and immune crosstalk (e.g., Th17). This leads to gut barrier dysfunction, systemic inflammation, and metabolic disturbances, contributing to diverse diseases beyond the oral cavity. Evidence supports causal links with conditions including rheumatoid arthritis, cardiovascular diseases, neurodegenerative disorders, metabolic syndrome, and gastrointestinal cancers. Emerging diagnostic tools exploit these oral pathogens as biomarkers for non-invasive disease detection. Therapeutic strategies, such as probiotics, dietary interventions, and periodontal therapy, target this axis to restore microbial homeostasis and ameliorate systemic inflammation. Future research must focus on longitudinal human studies and multi-omics approaches to elucidate mechanistic details and develop effective clinical interventions for preventing and managing systemic diseases linked to oral-gut microbial dysbiosis.},
}

Humans
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Mouth/microbiology
Inflammation/microbiology
Probiotics
Animals
Fusobacterium nucleatum/pathogenicity

@article {pmid41837339,
year = {2026},
author = {Jo, TS and Doi, H},
title = {Does Allometric Scaling Improve Estimates of Population Abundance Based on Environmental DNA?.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70303},
doi = {10.1111/mec.70303},
pmid = {41837339},
issn = {1365-294X},
support = {JP22J00439//Grant-in-Aid for JSPS Research Fellows/ ; JP22KJ3043//Grant-in-Aid for JSPS Research Fellows/ ; },
mesh = {*DNA, Environmental/analysis ; Population Density ; Animals ; Body Size ; Biodiversity ; *Genetics, Population/methods ; },
abstract = {Despite the popularity of environmental DNA (eDNA) analysis for non-invasive, cost-effective monitoring of aquatic biodiversity, its application for population abundance estimation is in its infancy. One of the uncertainties in eDNA-based abundance estimation surrounds the process of eDNA production: large individuals may produce less eDNA per unit body mass than smaller conspecifics, and there may be an allometric (power-law) relationship between the amount of eDNA released and body mass. Although integrating allometric scaling in eDNA production could refine eDNA-based abundance estimation, this theoretical framework may have a complex relationship with observed eDNA concentrations, especially in natural environments. We conducted a literature search to summarise previous studies that estimated population abundance using a combination of eDNA concentrations and allometric scaling frameworks, and found that allometry improved abundance estimates in only 5 of 12 studies. This did not seem to depend on the type of environment being studied, or the type of eDNA assay that was used. We discuss biological and technical factors that may help to explain the inconsistent allometric relationship between eDNA production and population abundance. We suggest that allometric scaling may be helpful when (i) the target populations exhibit substantial body size variation and (ii) species-specific scaling coefficients are available. However, our review shows that knowledge gaps remain in our understanding of abundance estimates based on eDNA, regardless of whether allometric relationships are factored into analyses.},
}

*DNA, Environmental/analysis
Population Density
Animals
Body Size
Biodiversity
*Genetics, Population/methods

@article {pmid41838875,
year = {2026},
author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C},
title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag119},
pmid = {41838875},
issn = {1477-4054},
support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Databases, Genetic ; *Software ; Computational Biology/methods ; Algorithms ; },
abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.},
}

*Metagenomics/methods
*Metagenome
Humans
Databases, Genetic
*Software
Computational Biology/methods
Algorithms

@article {pmid41795579,
year = {2026},
author = {Jin, X and Chen, X and Cao, X and Xiao, Z and Liu, Y and Wang, Z},
title = {Multi-omics analyses reveal combined toxic mechanisms of tricresyl phosphate and TiO2 nanoparticle on Daphnia magna.},
journal = {Journal of environmental management},
volume = {403},
number = {},
pages = {129224},
doi = {10.1016/j.jenvman.2026.129224},
pmid = {41795579},
issn = {1095-8630},
mesh = {Animals ; *Daphnia/drug effects ; *Titanium/toxicity ; *Nanoparticles/toxicity ; Daphnia magna ; Multiomics ; },
abstract = {In this study, the combined toxicity and mechanism of tricresyl phosphate (TCP) and nano-TiO2 to Daphnia magna were investigated. Results showed that the exposure of TCP at 50 μg/L and nano-TiO2 at 500 μg/L significantly inhibited the growth of Daphnia magna by 19.9 and 8.38% based on the body length, respectively. Co-exposure of TCP and nano-TiO2 exhibited synergistic effect on the growth of Daphnia magna, where the growth inhibition in TCP + nano-TiO2 treatment was 14.64% greater than that in TCP alone treatment. Mechanistically, (1) co-exposure of TCP and nano-TiO2 had greater alteration in bacterial community structure in Daphnia magna; (2) metabolomics results indicated that TCP + nano-TiO2 induced significant disruption to amino acids metabolism, nucleotide metabolism, and carbohydrate metabolism pathways in Daphnia magna; (3) proteomic analysis revealed that the co-exposure of TCP and nano-TiO2 triggered a greater downregulation of proteins (e.g., ribosomal proteins, RNA-binding protein, and citrate synthase) in amino acids metabolism, nucleotide metabolism, and energy metabolism compared with TCP alone treatment. Additionally, the co-exposure of TCP and nano-TiO2 exacerbated oxidative damage and disturbed antioxidant defense systems in Daphnia magna. Our findings reveal that the combined toxicity of nanoparticle and TCP should be considered for realistic evaluations of emerging contaminants.},
}

Animals
*Daphnia/drug effects
*Titanium/toxicity
*Nanoparticles/toxicity
Daphnia magna
Multiomics

@article {pmid41826799,
year = {2026},
author = {Chen, H and Shu, J and Mudappathi, R and Li, E and Wang, P and Bergsagel, L and Yang, P and Sun, Z and Zhao, L and Shi, C and Townsend, JP and Maley, C and Liu, L},
title = {Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag127},
pmid = {41826799},
issn = {1367-4811},
abstract = {MOTIVATION: Intratumor heterogeneity arises from ongoing somatic evolution and complicates cancer diagnosis, prognosis, and treatment. Reconstructing evolutionary dynamics typically requires spatiotemporal samples, which are often unavailable in clinical settings. Computational approaches that can infer tumor evolutionary history from single-timepoint bulk sequencing data remain limited.

RESULTS: We present TEATIME (estimating evolutionary events through single-timepoint sequencing), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric-fitness diversity-which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types.

AVAILABILITY: R implementation of TEATIME is available on GitHub (https://github.com/liliulab/TEATIME) and Zenodo (https://zenodo.org/records/17422174).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid41831075,
year = {2026},
author = {Thoker, IA and Shafi Bhat, M and Shah, SA and Khanday, AA and Parrey, HA and Akbar, M and Lone, FA},
title = {Evaluating Challenges and Opportunities to Boost Forest Productivity in the Kashmir Himalayas.},
journal = {Environmental management},
volume = {76},
number = {4},
pages = {},
pmid = {41831075},
issn = {1432-1009},
mesh = {*Forests ; *Conservation of Natural Resources/methods/economics ; *Forestry/methods/economics ; India ; Biodiversity ; Geographic Information Systems ; Himalayas ; },
abstract = {Forests are vital ecosystems that sustain biodiversity, regulate climate, and support local livelihoods. However, in the Kashmir Himalayas, forest productivity faces multiple constraints, including financial limitations, population pressure, land-use changes, and political instability. This study employs expert-based assessments and the Garrett ranking method to systematically evaluate the key challenges and opportunities for improving forest resource productivity in the region. Findings reveal that financial limitations (Mean Garrett Score [MGS] 70.80; R1), increasing population pressure (MGS 68.70; R2), and political volatility (MGS 65.53; R3) are the most significant bottlenecks, driving degradation and resource depletion. However, there are opportunities in terms of technological interventions such as Geographic Information Systems (GIS), Remote Sensing (RS), and Artificial Intelligence (AI) (MGS 71.33; R1), the launch of holistic research and development projects (MGS 68.50; R2), Participatory Forest Management (PFM) (MGS 66.10; R3), and the integration of agroforestry (MGS 60.43; R4), which could neutralize the constraints and boost the overall forest productivity in this fragile Himalayan region. Cashing in on these opportunities by adopting multipronged strategies could help in ecological restoration, real-time monitoring of forest health, improving forest cover and density, protecting wildlife, and enhancing the livelihoods of forest dwellers in the region. Encouraging research collaborations among forest agencies and skill development programmes for officials provides pathways to optimize resource management, ensuring socio-economic benefits for communities. Sustainable forest management is crucial for balancing conservation and economic needs while enhancing ecological resilience. The study highlights the need for a multi-stakeholder approach, offering insights for policymakers in shaping future forestry strategies.},
}

*Forests
*Conservation of Natural Resources/methods/economics
*Forestry/methods/economics
India
Biodiversity
Geographic Information Systems
Himalayas

@article {pmid41831867,
year = {2026},
author = {Sun, Z and Han, A and Li, J and Chen, W and Mao, J and Li, R and Shi, J and Yan, X and Yan, C},
title = {Involvement of gut microbiota in sub-chronic chlorantraniliprole-induced metabolic alteration in chironomid larvae (Propsilocerus akamusi): Evidence from multi-omics, histopathological and biochemical analysis.},
journal = {Pesticide biochemistry and physiology},
volume = {219},
number = {},
pages = {106999},
doi = {10.1016/j.pestbp.2026.106999},
pmid = {41831867},
issn = {1095-9939},
mesh = {Animals ; *Chironomidae/drug effects/microbiology/metabolism ; *ortho-Aminobenzoates/toxicity ; Larva/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Insecticides/toxicity ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {The widespread use and persistence of the insecticide chlorantraniliprole (CAP) in aquatic ecosystems poses a significant risk to non-target organisms. As gut microbiomes are increasingly considered as a critical mediator of host fitness, we investigated its role in the physiological response of chironomid larvae (Propsilocerus akamusi) to sub-chronic CAP exposure. Our results showed that LC10 and LC50 concentration of CAP treatment induced gut microbial dysbiosis, characterized by the remarkable alteration of community composition and bacterial interconnection networks. Histopathological and biochemical assays showed that CAP exposure distorted the architecture of larval midgut, along with stimulated oxidative stress and impaired detoxifying processes. This was accompanied by a proliferation of opportunistic pathogen Aeromonas in the gut and hemolymph. Integrated analysis further confirmed that the significant decline of beneficial bacteria (e.g. Tyzzerella) was linked to the impairment of aromatic and branched-chain amino acid metabolism. Concurrently, the proliferation of opportunistic pathogens, specifically Aeromonas, was associated with the disruption of glycerophospholipid and purine metabolism, with greater severity at LC50 dosage. Key genes, such as uricase, involved in these pathways were validated by transcriptome and RT-qPCR analysis. Notably, the pathogenic displacement of the genus Tyzzerella induced a compensatory activation of the TCA cycle in the LC50 group and triggered an upregulation of prostaglandin H2 in both groups, mounting compensatory immune and energetic defenses. Our study illustrated potential gut microbiota-modulated molecular mechanisms that underpin pesticide toxicity and host defense in chironomid larvae, providing a systematic framework for assessing the ecological impact of pesticides on aquatic invertebrates.},
}

Animals
*Chironomidae/drug effects/microbiology/metabolism
*ortho-Aminobenzoates/toxicity
Larva/drug effects/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
*Insecticides/toxicity
Oxidative Stress/drug effects
Multiomics

@article {pmid41826531,
year = {2026},
author = {Eckertová, T and Palyzová, A and Műllerová, M and Řezanka, T},
title = {Radioactive Springs and Archaeal Life in Deep Groundwater Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02720-7},
pmid = {41826531},
issn = {1432-184X},
support = {(VEGA project No. 1/0019/22//Scientific Grant Agency/ ; CZ.02.01.01/00/22_008/0004597//Grant Talking Microbes/ ; APVV-21-0356//Slovak Research and Development Agency/ ; RVO 61388971//Institutional Research Concept/ ; },
}

@article {pmid41821017,
year = {2026},
author = {Marra, M and Rotunno, S and Frascati, F and Pierro, R and Hammond, J and Vaira, AM and Miozzi, L},
title = {The analysis of the virome associated with Freesia refracta plants with necrotic disorder sheds new light on the phylogenetic relationships in the Konkoviridae and Yueviridae families.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {},
pmid = {41821017},
issn = {1743-422X},
support = {EVA-Global project, n. 871029//European Union's Horizon 2020/ ; EVA-Global project, n. 871029//European Union's Horizon 2020/ ; EVA-Global project, n. 871029//European Union's Horizon 2020/ ; Project SUS-MIRRI, n. IR0000005//European Commission-NextGenerationEU/ ; },
mesh = {*Phylogeny ; *Plant Diseases/virology ; *Virome ; Italy ; High-Throughput Nucleotide Sequencing ; *Plant Viruses/genetics/classification/isolation & purification ; Plant Leaves/virology ; RNA, Viral/genetics ; Computational Biology ; Genome, Viral ; },
abstract = {BACKGROUND: The necrotic disorder of freesia, first described in 1970 in Northern Europe, is still affecting freesia cultivation globally. Although several viruses have been listed as possible causal agents, the etiology of the disease is still not clear and is possibly linked to a combination of different factors. In this study, a high-throughput sequencing (HTS) virome analysis was performed on total RNA extracts derived from symptomatic freesia leaves.

METHODS: Freesia leaves showing necrotic disorder symptoms were collected in the Liguria region (Northwestern Italy) in 2011, 2014 and 2022. Total RNA was extracted and sent to specialized companies for rRNA-depletion library construction and Illumina sequencing. Ad hoc bioinformatics and phylogenetic analyses were performed on HTS data in order to identify and characterize plant viral entities. The Serratus Project Database was used to explore publicly available metatranscriptomic datasets with the aim of expanding selected viral families.

RESULTS: Freesia konkovirus 1, a novel virus putatively belonging to the recently ratified Konkoviridae family was identified and characterized. The family was further expanded through public metatranscriptomic data analyses; its phylogeny was investigated, and new genera were proposed. Moreover, a novel virus, putatively belonging to the Yueviridae family, was partially characterized, and its phylogenetic position was discussed.

CONCLUSIONS: This is the first untargeted HTS virome analysis of freesia necrotic disorder. Through a combined wet-lab and in silico approach, we identified unknown novel viruses, increasing the current knowledge of the diversity of viral agents that infect freesia, expanding and clarifying the phylogenesis of the very recently ratified families of Konkoviridae and Yueviridae, and highlighting possibly new actors in the freesia necrotic disorder.},
}

*Phylogeny
*Plant Diseases/virology
*Virome
Italy
High-Throughput Nucleotide Sequencing
*Plant Viruses/genetics/classification/isolation & purification
Plant Leaves/virology
RNA, Viral/genetics
Computational Biology
Genome, Viral

@article {pmid41814333,
year = {2026},
author = {Noviello, C and Bianchi, FP and Lobifaro, A and Pinelli, N and Riformato, G and Tafuri, S and , and Migliore, G and Stefanizzi, P},
title = {The role of hospitals in monitoring the emergency: the experience of "Sentinel network" of the Italian Federation of Health Trusts.},
journal = {BMC health services research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12913-026-14279-7},
pmid = {41814333},
issn = {1472-6963},
abstract = {The COVID-19 pandemic showed few weak points in health-system resilience and highlighted the need to strengthen surveillance capacities. In Italy, the Federation of Health Trusts (FIASO) established the Sentinel Hospital Network (SHNet) to monitor COVID-19 hospitalizations and support operational decision-making. A multicentre ecological study was conducted across 21 hospitals (November 2021-March 2023), collecting weekly data on admissions, vaccination status, and classification of cases as for or with COVID-19. Trends were compared with national surveillance from the Istituto Superiore di Sanità (ISS). SHNet recorded 48,117 admissions in 2022. Basically vaccination reduced the severe disease, with an 87% decrease in ICU admissions for COVID-19. Hospitalizations with COVID-19 showed limited variation. Strong correlation with ISS trends confirmed SHNet reliability. SHNet provided timely, clinically detailed data complementing national surveillance and improved understanding of hospital burden. Sentinel surveillance represents a preacious tool for preparedness, enabling rapid response, resource optimization, and resilience in future health emergencies.},
}

@article {pmid41762988,
year = {2026},
author = {Dongye, C and Wang, S and Chen, X and Li, C and Zhao, Y and Chan, TD and Boukherroub, R and Chen, X},
title = {Skin toxicity of liquid crystal monomers (LCMs): Mitochondrial dysfunction and metabolic dysregulation revealed by integrated multi-omics analysis.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119953},
doi = {10.1016/j.ecoenv.2026.119953},
pmid = {41762988},
issn = {1090-2414},
mesh = {Animals ; *Skin/drug effects ; Mice ; *Liquid Crystals/toxicity ; *Mitochondria/drug effects ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Liquid crystal monomers (LCMs), as core components of liquid crystal displays (LCDs), are emerging as environmental materials due to their widespread use and potential for human and ecological exposure. Even as inquiries pertaining to the environmental and health risks of LCMs are progressing, their direct toxic effects on human organs and ecosystems persist in being inadequately comprehended. The present research underscores the hazards entailed by prolonged LCMs exposure, with specific reference to skin cells and animal models, under daily exposure magnitudes. This study reveals that long-term LCMs exposure disrupts mitochondrial function in skin cells, triggers inflammatory pathways (TNF signaling), and downregulates critical proteins (PLOD2, DDIT4) and metabolites (ATP, glutathione), indicating oxidative stress and cellular dysfunction. In vivo experiments further demonstrate histopathological damage in mouse skin, including disordered skin appendages and adipose disorganization, highlighting LCMs' hazardous potential. Multi-omics analysis links LCMs exposure to diseases such as lung cancer and Alzheimer's, while untargeted metabolomics identifies β-alanylleucine downregulation as a promising biomarker for LCM-induced toxicity. Given LCD e-waste growth, improper disposal releases LCMs, risking ecosystem bioaccumulation. These findings underscore the need for stricter regulation of LCMs throughout their lifecycle-from production to waste management-to mitigate ecological and health risks, with β-alanylleucine serving as a potential monitoring tool for environmental contamination.},
}

Animals
*Skin/drug effects
Mice
*Liquid Crystals/toxicity
*Mitochondria/drug effects
Metabolomics
Oxidative Stress/drug effects
Multiomics

@article {pmid41730398,
year = {2026},
author = {Yang, J and Huang, T and Huang, Y and Yu, M and Jiaba, W and Su, R and Liu, L and Guan, L},
title = {Multi-omics dissection of lignan diversity and therapeutic potential in Ocimum: Identification of diphyllin as an anti-inflammatory agent targeting TNF-α signaling.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121412},
doi = {10.1016/j.jep.2026.121412},
pmid = {41730398},
issn = {1872-7573},
mesh = {*Lignans/pharmacology/chemistry/metabolism/isolation & purification ; *Anti-Inflammatory Agents/pharmacology/isolation & purification/therapeutic use ; Animals ; *Tumor Necrosis Factor-alpha/metabolism ; Molecular Docking Simulation ; Signal Transduction/drug effects ; *Ocimum/chemistry/genetics ; Mice ; Male ; Network Pharmacology ; Lipopolysaccharides ; Mice, Inbred C57BL ; Inflammation/drug therapy ; Molecular Dynamics Simulation ; Multiomics ; },
abstract = {Ocimum species have long been used in traditional medicine systems across Asia and Africa for managing inflammatory disorders, gastrointestinal disturbances, and chronic diseases. However, despite their well-recognized medicinal importance, the metabolic diversity and therapeutic potential of Ocimum lignans remain insufficiently explored.

AIM OF THE STUDY: To systematically characterize lignan metabolites across multiple Ocimum accessions, elucidate the genetic basis underlying their biosynthesis, predict their multi-target pharmacological activities, and experimentally evaluate their anti-inflammatory efficacy.

MATERIALS AND METHODS: Ten Ocimum accessions were profiled using UPLC-MS/MS to construct a comprehensive lignan metabolite spectrum. Network pharmacology, molecular docking, and molecular dynamics simulations were performed to predict lignan-target interactions and assess binding stability. RNA-seq analysis was used to reconstruct the diphyllin biosynthetic pathway and identify key regulatory genes. The anti-inflammatory activity of diphyllin was validated using an LPS-induced intestinal inflammation model.

RESULTS: A total of 63 lignans were identified, with 62 exhibiting significant differential accumulation among accessions. Network pharmacology predicted 422 putative targets for 29 lignans, with 14 core targets (e.g., BCL2, EGFR, TNF) enriched in cancer-, inflammation-, and metabolism-related pathways. Docking and molecular dynamics simulations confirmed strong and stable ligand-protein interactions, particularly for diphyllin. Transcriptomic analysis revealed a complete lignan biosynthetic pathway and highlighted the central involvement of CAD family genes in diphyllin formation. In vivo experiments demonstrated that diphyllin significantly reduced inflammatory responses and improved intestinal barrier integrity by suppressing TNF-α signaling.

CONCLUSIONS: This multi-omics investigation reveals substantial metabolic diversity and mechanistic complexity underlying lignan biosynthesis and bioactivity in Ocimum. The integration of phytochemical profiling, systems pharmacology, and in vivo validation provides strong evidence supporting the development of Ocimum lignans, especially diphyllin as promising anti-inflammatory agents for functional foods and natural therapeutics.},
}

*Lignans/pharmacology/chemistry/metabolism/isolation & purification
*Anti-Inflammatory Agents/pharmacology/isolation & purification/therapeutic use
Animals
*Tumor Necrosis Factor-alpha/metabolism
Molecular Docking Simulation
Signal Transduction/drug effects
*Ocimum/chemistry/genetics
Mice
Male
Network Pharmacology
Lipopolysaccharides
Mice, Inbred C57BL
Inflammation/drug therapy
Molecular Dynamics Simulation
Multiomics

@article {pmid41112753,
year = {2025},
author = {Suzuki, A and Hisamoto, S and Sakamoto, Y},
title = {Dynamics of the hindgut microbiota of the Japanese honey bees (Apis cerana japonica) throughout the overwintering period.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20050},
pmid = {41112753},
issn = {2167-8359},
mesh = {*Bees/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; Seasons ; Animals ; *Cold Temperature/adverse effects ; Japan ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/isolation & purification ; Datasets as Topic ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; },
abstract = {Honey bees play crucial roles as pollinators in natural, agricultural, and ecological systems. The role of gut microbiota in the overwinter survival of honey bees is gaining attention. Compared with Western honey bees (Apis mellifera), Eastern honey bees (Apis cerana) are more tolerant to low-temperature stress. This study compared the hindgut microbiota of the Japanese honey bees (Apis cerana japonica), a subspecies of A. cerana, during the overwintering period (December) with that before overwintering (October) and after overwintering (March) to estimate beneficial hindgut bacteria contributing to survival during the overwintering period. Overall, the hindgut microbiota of A. c. japonica was occupied by Actinobacteriota, Bacteroidota, Firmicutes, and Proteobacteria at the phylum level and Apibacter, Bifidobacterium, Bombilactobacillus, Gilliamella, Lactobacillus, and Snodgrassella at the genus level. The hindgut microbiota composition of A. c. japonica was similar to that of A. cerana in other regions, suggesting that phylogeny influenced the composition. Many sequences assigned to these six core genera showed <98.7% similarity to type strains, indicating potential novel bacterial species. The relative abundance of Bifidobacterium, Bombilactobacillus, and Lactobacillus was higher during overwintering than in other periods. Our findings highlight changes in the core bacteria of the hindgut microbiota of A. c. japonica during overwintering and also suggest the presence of novel candidate bacterial species. The roles of the bacteria that were increased during the overwintering period require further elucidation.},
}

*Bees/microbiology/physiology
*Gastrointestinal Microbiome/physiology
Seasons
Animals
*Cold Temperature/adverse effects
Japan
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics/isolation & purification
Datasets as Topic
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA

@article {pmid41808579,
year = {2026},
author = {Auerbach, BM and Jackson, FLC and Berry, SD and Blakey, ML and Caldwell, J and Clinton, C and Graves, JL and Jones, JB and Lofaro, EM and Malhi, RS and Mosley, CV and Stubblefield, PR},
title = {AABA Task Force on the Ethical Study of Human Remains Recommendations: Proposal for the Management and Oversight of Community Partnership and Ethical Stewardship of Human Remains.},
journal = {American journal of biological anthropology},
volume = {189},
number = {3},
pages = {e70213},
pmid = {41808579},
issn = {2692-7691},
mesh = {Humans ; United States ; Advisory Committees ; Black or African American ; Societies, Scientific ; White ; },
abstract = {Ethically responsible and culturally acceptable management, study, and stewardship of legacy skeletal and other human remains currently held and managed in scientific institutions is a longstanding concern that, over the length of these collections' existence, has been exiguously addressed. Most recently, the ethical treatment of legacy collections of individuals from the African American community in the United States has been especially highlighted. The American Association of Biological Anthropologists (AABA) created a Presidential Task Force to address these concerns about legacy collections in 2022 by drafting practices and recommendations for policies to be adopted by the AABA and sibling organizations. We report on the first ever convergent analysis of research priorities and perspectives on these topics from the communities of biological anthropologists and a national cross-section of African Americans. Based on the surveys and discussions with these communities, all groups expressed a desire to enter a mutual, formal partnership where descendant communities are empowered to make decisions about the study and disposition of legacy collections. Our recommendations focus on promoting dialogue between parties involved through partnerships where desired. To make this possible, institutions should inventory and determine provenance of remains in legacy collections, ascertain the identity of descendant communities, and contact those communities using guidelines we provide. We argue that a default position taken by researchers is that no research need occur without the explicit consent of relevant descendant communities or communities of care. Examples of successful community partnerships are provided, along with new practices in ethical engagement with descendant communities.},
}

Humans
United States
Advisory Committees
Black or African American
Societies, Scientific
White

@article {pmid41759316,
year = {2026},
author = {Zhang, J and Zhang, Z and Shen, Z and Yu, Z and Chen, J and Zeng, L and Li, D and Yan, X and Li, B and Wong, JWC},
title = {PDG_DB: A comprehensive database unveils environmental distribution patterns of plastic-degrading genes via large-scale multi-omic data analysis.},
journal = {Water research},
volume = {296},
number = {},
pages = {125619},
doi = {10.1016/j.watres.2026.125619},
pmid = {41759316},
issn = {1879-2448},
mesh = {*Plastics/metabolism ; Biodegradation, Environmental ; Multiomics ; },
abstract = {Plastic pollution has become a global environmental crisis, driving urgent research into plastic-degrading enzymes for achieving efficient green transformation and recycling of plastic waste. However, current plastic-degrading gene (PDG) databases remain fragmented and incomplete. Simultaneously, research has predominantly focused on laboratory-isolated strains with the limited exploration of the vast reservoir of PDGs in environmental metagenomes. To address these limitations, we employed large-scale environmental multi-omics analysis to systematically mine and characterize PDGs across diverse ecosystems. We constructed PDG_DB (https://github.com/Z-bioinfo/PDG_DB), a comprehensive PDG database containing 341 experimentally validated sequences categorized by substrate specificity. Large-scale multi-omics analysis across environmental samples identified 7,111 PDGs (3,612 non-redundant), with polyhydroxyalkanoate (PHAs) degrading genes predominating. Molecular docking revealed that novel putative PDGs for PHA degradation exhibited stronger binding affinity compared to known PDGs, demonstrating the necessity of mining novel enzymes from environmental sources. Most PDGs were bacterial, primarily from Pseudomonadota, with the genus Pseudomonas showing the broadest degradation range. Our global analysis of 5,466 datasets revealed high PDG abundance in East Asia, North Europe, America, and the oceans. Unexpectedly, drinking water systems harbored the highest PDG abundance, challenging assumptions about plastic contamination in potable water. PDG distribution varied by environment: soil favored genes for non-biodegradable plastics, while wastewater systems preferred those for biodegradable plastics. Metatranscriptomic analysis showed the highest PDG activity in marine environments. This work provides a comprehensive resource for PDGs, revealing distinctive global distribution patterns with drinking water systems as an unexpected reservoir. PDG_DB serves as a foundational database for identifying PDGs, facilitating future environmental monitoring and biotechnology applications.},
}

*Plastics/metabolism
Biodegradation, Environmental
Multiomics

@article {pmid41722400,
year = {2026},
author = {Wang, S and Wan, S and Shen, Q and Yue, L and Wang, J and Zhou, M and Li, Y and Tang, B},
title = {Cadmium disrupts energy metabolism in the Harmonia axyridis via mediating trehalose metabolism pathway: A multi-omics analysis.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141412},
doi = {10.1016/j.jhazmat.2026.141412},
pmid = {41722400},
issn = {1873-3336},
mesh = {Animals ; *Cadmium/toxicity ; *Trehalose/metabolism ; *Energy Metabolism/drug effects ; *Coleoptera/drug effects/metabolism/genetics ; Larva/drug effects/metabolism/genetics ; Transcriptome/drug effects ; Metabolomics ; Multiomics ; },
abstract = {Cadmium (Cd), a ubiquitous heavy metal pollutant, threatens the ecological functions of the natural enemy insect Harmonia axyridis, though the molecular mechanisms of its toxicity remain poorly understood. Here, we first determined the 48-h median lethal concentration (LC50) of Cd for third‑instar H. axyridis larvae as 7.667 mg/mL. Using a multi‑omics approach, we then analyzed larval responses to injected Cd stress at LC25, LC50, and LC75 concentrations. Transcriptomics revealed 1986, 1471, and 1433 differentially expressed genes (DEGs) in the respective treatment groups, including down‑regulated genes encoding α,α‑trehalase (TRE) and maltase‑glucoamylase involved in carbohydrate metabolism. Metabolomics identified 907, 294, and 511 differential metabolites (DMs) across the three Cd exposures, with significant accumulation of sucrose and sucrose 6'‑phosphate in the LC50 group. Integrated omics analysis showed that both DEGs and DMs were co‑enriched in starch and sucrose metabolism and galactose metabolism pathways. Furthermore, Cd transferred through the soil‑plant‑aphid‑ladybug food chain disrupted trehalose metabolism, leading to reduced carbohydrate levels, suppressed trehalase activity, and altered expression of key metabolic genes. Together, these results indicate that Cd‑induced downregulation of trehalose‑related genes causes upstream carbohydrate accumulation (e.g., sucrose) and disrupts the trehalose metabolic pathway, ultimately impairing energy homeostasis. This study uncovers a novel mechanism by which heavy metal pollution affects natural enemy insects via metabolic interference. Our findings highlight the potential disruption of pest control in agroecosystems under heavy metal stress and provide critical molecular targets for assessing the ecological risk of Cd pollution on beneficial insects.},
}

Animals
*Cadmium/toxicity
*Trehalose/metabolism
*Energy Metabolism/drug effects
*Coleoptera/drug effects/metabolism/genetics
Larva/drug effects/metabolism/genetics
Transcriptome/drug effects
Metabolomics
Multiomics

@article {pmid41680303,
year = {2026},
author = {Soltani, A and Memmert, D and Rezaie, R and Nazemzadegan, G and Koushkie Jahromi, M},
title = {Comparing the effect of mental fatigue-inducing models on selected cognitive and technical performance aspects in young soccer players.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41680303},
issn = {2045-2322},
support = {0INB3M1899//Shiraz University/ ; },
abstract = {Mental fatigue is a well-documented performance inhibitor in team sports, Therefore, identifying strategies to attenuate mental fatigue seems necessary. This study aimed to evaluate and compare four distinct training models—Modified Stroop, SAFT[90], T-SAFT[90], and a combined T-SAFT[90] + Stroop protocol—to identify the most effective method for inducing mental fatigue under controlled laboratory conditions, as a potential model for brain endurance training (BET) research in young soccer players. Fifteen male players (aged 16–18) participated in a randomized cross-over study. Mental fatigue was assessed via a Visual Analogue Scale (VAS; primary outcome), cognitive performance (secondary outcomes) was evaluated through response time, response accuracy, working memory capacity, visual Scanning Identification, and auditory pattern recognition. Technical performance was measured using penalty time, movement time and passing accuracy in the Loughborough Soccer Passing Test (LSPT; primary outcomes). All protocols significantly increased mental fatigue, with the largest effect observed in the combined T-SAFT[90] + Stroop model. Response accuracy declined across all models, while response time worsened in the Stroop and T-SAFT[90] conditions. Penalty time increased in the Stroop and T-SAFT[90] protocols, whereas passing accuracy decreased most significantly in the combined model. In summary, under standardized, controlled conditions, the combined cognitive-physical training model induced the highest mental fatigue and most consistently altered cognitive and technical performance. These findings provide preliminary evidence supporting its potential as a BET model for research and structured training environments, though ecological validation in real soccer contexts remains necessary.},
}

@article {pmid41665259,
year = {2025},
author = {Gaisin, VA and Hadjicharalambous, C and Mujakić, I and Villena-Alemany, C and Li, J and Koblížek, M and Pilhofer, M},
title = {Thermophilic bacteria employ a contractile injection system in hot spring microbial mats.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag021},
pmid = {41665259},
issn = {1751-7370},
support = {CZ.02.01.01/00/22_008/0004624//OP JAK project Photomachines/ ; CoG 101000232/ERC_/European Research Council/International ; },
mesh = {*Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; *Chloroflexi/genetics/physiology/classification/metabolism ; Cryoelectron Microscopy ; Phylogeny ; Metagenomics ; *Bacteria/genetics ; Computational Biology ; Proteomics ; },
abstract = {Bacterial contractile injection systems (CISs) are multiprotein complexes that facilitate the bacterial response to environmental factors or interactions with other organisms. Multiple novel CISs have been characterised in laboratory bacterial cultures recently; however, studying CISs in the context of the native microbial community remains challenging. Here, we present an approach to characterise a bioinformatically predicted CIS by directly analysing bacterial cells from their natural environment. Using cryo-focused ion beam milling and cryo-electron tomography (cryoET) imaging, guided by 16S rRNA gene amplicon sequencing, we discovered that thermophilic Chloroflexota bacteria produce intracellular CIS particles in a natural hot spring microbial mat. We then found a niche-specific production of CIS in the structured microbial community using an approach combining metagenomics, proteomics, and immunogold staining. Bioinformatic analysis and imaging revealed CISs in other extremophilic Chloroflexota and Deinococcota. This Chloroflexota/Deinococcota CIS lineage shows phylogenetic and structural similarity to previously described cytoplasmic CIS from Streptomyces and probably shares the same cytoplasmic mode of action. Our integrated environmental cryoET approach is suitable for discovering and characterising novel macromolecular complexes in environmental samples.},
}

*Hot Springs/microbiology
RNA, Ribosomal, 16S/genetics
*Chloroflexi/genetics/physiology/classification/metabolism
Cryoelectron Microscopy
Phylogeny
Metagenomics
*Bacteria/genetics
Computational Biology
Proteomics

@article {pmid41639124,
year = {2026},
author = {Goicolea, T and Morales-Barbero, J and García-Viñas, JI and Gastón, A and Aroca-Fernández, MJ and Calleja, JA and Moreno, JC and Ramos-Gutiérrez, I and Rodríguez, MÁ and Lima, H and Broennimann, O and Guisan, A and Adde, A and Pérez-Latorre, AV and Mateo, RG},
title = {A unified plant ecology database for Spain.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41639124},
issn = {2052-4463},
mesh = {Spain ; *Plants/classification ; *Databases, Factual ; Conservation of Natural Resources ; Biodiversity ; Ecology ; Ecosystem ; },
abstract = {We present a new database providing spatial data to support plant ecological research and conservation throughout mainland Spain. It integrates high-resolution spatial data of four main categories: (I) plant occurrence data, (II) environmental variables, (III) species distribution models, and (IV) thematic maps for conservation and management. The occurrence dataset includes georeferenced records for 81 tree and 101 shrub native species, and atlas data for 6,456 vascular plants and 1,252 bryophytes. Environmental variables include climatic, edaphic, hydrological, and solar, factors influencing plant distribution. Species distribution models are available for all the trees and shrubs (182 species). Thematic maps include species richness for woody and protected plants, distribution of vegetation types, and forest connectivity. All climatic variables, models, and thematic maps are projected under current and four future climate scenarios (2070-2100). The database is openly available on Zenodo.},
}

Spain
*Plants/classification
*Databases, Factual
Conservation of Natural Resources
Biodiversity
Ecology
Ecosystem

@article {pmid41805908,
year = {2026},
author = {Singh, P and Sheen, J and Saad-Roy, CM and Levy, MZ and Metcalf, CJE},
title = {Coevolution of host resistance and pathogen exploitation in a propagule-mediated infection model.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013999},
doi = {10.1371/journal.pcbi.1013999},
pmid = {41805908},
issn = {1553-7358},
abstract = {Host populations often face infection risk from pathogens that can persist in the environment as free-living propagules. We develop a population-level model to understand how host resistance - defined as reduced susceptibility to infection - evolves in response to the exploitation strategy of a pathogen where transmission occurs exclusively via environmental propagules. Using an adaptive dynamics framework, we analyze how the coevolution of host resistance and pathogen exploitation strategy unfolds under the following fitness costs: reduced survival associated with investment in resistance reflected by additional background mortality for the host; and reduced average lifespan represented by increased infected host mortality for the pathogen. Calculating individual host and pathogen invasion fitness expressions using standard invasion analysis, we track how stable levels of investment in host resistance vary across different infection scenarios. We found that costly resistance is disfavoured when pathogen encounters are excessively high, with maximal resistance selected at intermediate levels of transmission. Coevolutionary feedbacks between host resistance and pathogen exploitation can lead to diverse outcomes, including stable evolutionarily singular strategies and, under weakly accelerating costs, evolutionary branching that generates coexistence in the resistance trait. We further quantify how coevolution shapes the equilibrium density of free propagules, revealing conditions under which coevolution suppresses or amplifies pathogen prevalence in comparison to non-evolving scenarios. Overall, our model framework built on survival-based costs offers testable predictions for environmentally transmitted host-pathogen systems.},
}

@article {pmid41758887,
year = {2026},
author = {Kuo, HY and Kryazhimskiy, S},
title = {Putting BASIL in a BLT: A Bayesian filtering method for estimating the fitness effects of nascent adaptive mutations.},
journal = {PLoS computational biology},
volume = {22},
number = {2},
pages = {e1013946},
pmid = {41758887},
issn = {1553-7358},
mesh = {*Mutation/genetics ; Bayes Theorem ; *Genetic Fitness/genetics ; Computational Biology/methods ; *Models, Genetic ; *Adaptation, Physiological/genetics ; Computer Simulation ; Algorithms ; },
abstract = {The distribution of fitness effects (DFE) of new beneficial mutations is a key quantity that dictates the dynamics of adaptation. The barcode lineage tracking (BLT) approach is an important advance toward measuring DFEs. BLT experiments enable researchers to track the frequencies of ~105 barcoded lineages in large microbial populations and detect up to thousands of nascent beneficial mutations in a single experiment. However, reliably identifying adapted lineages and estimating the fitness effects of driver mutations remains a challenge because lineage dynamics are subject to demographic and measurement noise and competition with other lineages. We show that the commonly used Levy-Blundell method for analyzing BLT data and its improved version FitMut2 can produce biased fitness estimates, particularly if selection is strong. To address this problem, we develop a new method called BASIL (BAyesian Selection Inference for Lineage tracking data), which dynamically updates the belief distribution of each lineage's fitness and size based on the number of barcode reads. We calibrate BASIL's model of noise with new experimental data and find that noise variance scales non-linearly with lineage abundance. We test how BASIL and FitMut2 perform on simulated data and on down-sampled data from the original BLT data by Levy et al and find that BASIL is both more robust and more accurate than FitMut2. Our work paves the way for a systematic inference of the distribution of fitness effects of new beneficial mutations from BLT experiments in a variety of scenarios.},
}

*Mutation/genetics
Bayes Theorem
*Genetic Fitness/genetics
Computational Biology/methods
*Models, Genetic
*Adaptation, Physiological/genetics
Computer Simulation
Algorithms

@article {pmid40367332,
year = {2026},
author = {Rodríguez Hernández, JM and Chaparro Narváez, PE and Hidalgo Troya, A and Piñeros Garzón, FS},
title = {Undercounts stemming from misclassification derived from fatal injuries in traffic crashes in Colombia, 2010 to 2021.},
journal = {Traffic injury prevention},
volume = {27},
number = {3},
pages = {278-286},
doi = {10.1080/15389588.2025.2495863},
pmid = {40367332},
issn = {1538-957X},
mesh = {Humans ; Colombia/epidemiology ; *Accidents, Traffic/mortality/statistics & numerical data ; Male ; Adult ; Middle Aged ; Female ; Motorcycles/statistics & numerical data ; *Wounds and Injuries/mortality ; Adolescent ; Young Adult ; Pedestrians/statistics & numerical data ; Databases, Factual ; Bicycling/injuries/statistics & numerical data ; Aged ; Child ; },
abstract = {OBJECTIVES: To identify and address potential misclassification of traffic fatalities in Colombia from 2010 to 2021.

METHODS: For an ecological study, we employed national records and databases. A database was consolidated to include information on the fatality occurrence site, area, place of death, year of occurrence, marital status, age, and enrollment in social security. Generalized linear regression models were used to detect and adjust possible errors in records due to misclassification starting from existing data, allowing reclassification with a high probability of specific garbage codes being valid, potentially associated with mortality caused by traffic.

RESULTS: In 2010; there was a mortality rate of 13.3 deaths per 100,000 population, while in 2021; it was 15.1/per 100,000 population. In 2020; from the effects of pandemic-related confinement, the risk came down to 11.5/100.000 population. With the imputation, these records increased from 14.9 (2010) to 16.4 (2021); the most notable rise was among motorcyclists, who contributed 62%, with a marked increase in 2021:13/100.000 population, while pedestrians contributed 27.2%, cyclists: 4% and vehicle occupants: 6.5%.

CONCLUSIONS: Over the past decade, Colombia has stood out as one of the few countries worldwide that have been unable to reduce traffic-related mortality. The potential underestimation of the problem likely exacerbates this challenge due to record misclassification or measurement errors, which may be as high as 10%. Motorcyclists are particularly vulnerable, facing a significantly increased risk of death. To address this critical issue, cross-sectoral and inter-institutional policies, and plans are urgently needed to mitigate the high incidence of motorcycle fatalities and break the cycles of poverty and orphanhood they can cause.},
}

Humans
Colombia/epidemiology
*Accidents, Traffic/mortality/statistics & numerical data
Male
Adult
Middle Aged
Female
Motorcycles/statistics & numerical data
*Wounds and Injuries/mortality
Adolescent
Young Adult
Pedestrians/statistics & numerical data
Databases, Factual
Bicycling/injuries/statistics & numerical data
Aged
Child

@article {pmid37660825,
year = {2023},
author = {Yang, X and Xu, H and Lin, K and Tan, L and Wang, J},
title = {Multi-omics integration analysis of long-distance drifting process of green tides in the Yellow Sea simulated in a large-volume flowing water system.},
journal = {The Science of the total environment},
volume = {903},
number = {},
pages = {166697},
doi = {10.1016/j.scitotenv.2023.166697},
pmid = {37660825},
issn = {1879-1026},
mesh = {Seawater/chemistry ; China ; *Environmental Monitoring ; *Eutrophication ; Biomass ; Multiomics ; },
abstract = {The drifting process of U. prolifera were simulated in a large-volume flowing water system with conditions similar to the field in the Yellow Sea. Biomass and chl-a content per unit of U. prolifera were monitored in the flowing water system by simulating nutrients and temperature variations of seawaters from starting place to terminus of U. prolifera in the South Yellow Sea. According to the variations of nutrients during the drifting process, the floating process can be divided into three stages. Differentially expressed genes and differential metabolites in the three stages of U. prolifera drifting process were identified, which are mainly related to glycometabolism, nitrogen metabolism, and selenium compound metabolism. The process from Stage I to Stage II are mainly related to the translation and molecular function of biological processes, and the main differential metabolites are primary metabolites, whereas, from Stage II to Stage III, secondary metabolites start to increase, indicating that U. prolifera resisted environmental stress by increasing lipids and producing secondary metabolites. It will provide some guidance for the comprehensive interpretation of the biological basis and ecological mechanisms of the large-scale U. prolifera green tides in the Yellow Sea.},
}

Seawater/chemistry
China
*Environmental Monitoring
*Eutrophication
Biomass
Multiomics

@article {pmid37605971,
year = {2023},
author = {Forzieri, G and Dutrieux, LP and Elia, A and Eckhardt, B and Caudullo, G and Taboada, FÁ and Andriolo, A and Bălăcenoiu, F and Bastos, A and Buzatu, A and Dorado, FC and Dobrovolný, L and Duduman, ML and Fernandez-Carrillo, A and Hernández-Clemente, R and Hornero, A and Ionuț, S and Lombardero, MJ and Junttila, S and Lukeš, P and Marianelli, L and Mas, H and Mlčoušek, M and Mugnai, F and Nețoiu, C and Nikolov, C and Olenici, N and Olsson, PO and Paoli, F and Paraschiv, M and Patočka, Z and Pérez-Laorga, E and Quero, JL and Rüetschi, M and Stroheker, S and Nardi, D and Ferenčík, J and Battisti, A and Hartmann, H and Nistor, C and Cescatti, A and Beck, PSA},
title = {The Database of European Forest Insect and Disease Disturbances: DEFID2.},
journal = {Global change biology},
volume = {29},
number = {21},
pages = {6040-6065},
doi = {10.1111/gcb.16912},
pmid = {37605971},
issn = {1365-2486},
support = {101039567/ERC_/European Research Council/International ; },
mesh = {*Forests ; Animals ; *Insecta/physiology ; Europe ; Climate Change ; *Databases, Factual ; *Plant Diseases ; *Trees ; },
abstract = {Insect and disease outbreaks in forests are biotic disturbances that can profoundly alter ecosystem dynamics. In many parts of the world, these disturbance regimes are intensifying as the climate changes and shifts the distribution of species and biomes. As a result, key forest ecosystem services, such as carbon sequestration, regulation of water flows, wood production, protection of soils, and the conservation of biodiversity, could be increasingly compromised. Despite the relevance of these detrimental effects, there are currently no spatially detailed databases that record insect and disease disturbances on forests at the pan-European scale. Here, we present the new Database of European Forest Insect and Disease Disturbances (DEFID2). It comprises over 650,000 harmonized georeferenced records, mapped as polygons or points, of insects and disease disturbances that occurred between 1963 and 2021 in European forests. The records currently span eight different countries and were acquired through diverse methods (e.g., ground surveys, remote sensing techniques). The records in DEFID2 are described by a set of qualitative attributes, including severity and patterns of damage symptoms, agents, host tree species, climate-driven trigger factors, silvicultural practices, and eventual sanitary interventions. They are further complemented with a satellite-based quantitative characterization of the affected forest areas based on Landsat Normalized Burn Ratio time series, and damage metrics derived from them using the LandTrendr spectral-temporal segmentation algorithm (including onset, duration, magnitude, and rate of the disturbance), and possible interactions with windthrow and wildfire events. The DEFID2 database is a novel resource for many large-scale applications dealing with biotic disturbances. It offers a unique contribution to design networks of experiments, improve our understanding of ecological processes underlying biotic forest disturbances, monitor their dynamics, and enhance their representation in land-climate models. Further data sharing is encouraged to extend and improve the DEFID2 database continuously. The database is freely available at https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/DISTURBANCES/DEFID2/.},
}

*Forests
Animals
*Insecta/physiology
Europe
Climate Change
*Databases, Factual
*Plant Diseases
*Trees

@article {pmid41803388,
year = {2026},
author = {Yang, X and Tian, J and Ciais, P and Zhou, L and Reich, PB and Wu, J and Shang, J and Chave, J and Lamour, J and Maréchaux, I and Fu, YH and Chen, JM and Liu, J and Tao, S and Xiao, X and Xu, X and Su, Y and Zhang, H and Zhu, Z and Zhang, Y and Hao, D and Chen, L and Liu, Q and Lafortezza, R and Yan, K and Li, P and Li, X and Meir, P and Liu, H and Bonal, D and Nelson, BW and Tang, H and Wang, J and Yu, K and Yuan, W and Wang, S and Chen, X},
title = {Amazon rainforests are rejuvenating their canopies by producing more photosynthetically efficient young leaves under climate change.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41803388},
issn = {2055-0278},
abstract = {Leaf age structure strongly regulates canopy photosynthesis in Amazon rainforests yet its large-scale patterns and dynamics remain poorly understood. Here we map the fraction of leaf area of photosynthetically efficient young leaves (fyoung) using remote sensing data and assess its spatiotemporal variability from 2001 to 2023. We find that fyoung varies markedly with elevation and canopy height: tall or mountain forests (canopy ≥32 m or elevation ≥300 m) exhibit higher fyoung than short or lowland forests, reflecting higher leaf turnover driven by stronger radiation, greater atmospheric dryness and longer dry seasons. Across the basin, fyoung increased significantly in 85.2% of forests during 2001-2023, linked to decreasing precipitation, rising sunlight, intensifying atmospheric dryness and lengthening dry seasons. This widespread trend towards more juvenile leaves is projected to persist under future climate change. Our findings reveal a fundamental shift in Amazon leaf age structure and highlight its importance for predicting future photosynthetic responses in a warmer, drier climate.},
}

@article {pmid41802001,
year = {2026},
author = {Ersado, AE and Talluri, VK},
title = {GIS-based land suitability evaluation and multi-criteria decision analysis for sustainable enset (Ensete ventricosum (Welw.) Cheesman) cultivation in Hadiya Zone, Central Ethiopia.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344127},
doi = {10.1371/journal.pone.0344127},
pmid = {41802001},
issn = {1932-6203},
mesh = {Ethiopia ; *Geographic Information Systems ; *Crops, Agricultural/growth & development ; *Agriculture/methods ; Soil/chemistry ; *Decision Support Techniques ; *Conservation of Natural Resources ; },
abstract = {Land suitability analysis is a key approach for evaluating the potential of land resources for specific uses and for supporting sustainable agricultural planning. In Ethiopia, where agriculture forms the backbone of rural livelihoods, identifying suitable land for staple crops is essential to ensure food security and long-term productivity. This study evaluated the actual land suitability for enset (Ensete ventricosum) cultivation in the Hadiya Zone, Central Ethiopia, by systematically comparing the spatial distribution of key environmental factors with established enset crop requirement standards. For each parameter, spatial data were overlaid with enset-specific ecological thresholds derived from relevant literature and expert consultation. Based on the FAO land evaluation framework, all factors were classified into five suitability classes: Very Highly Suitable (S1), Highly Suitable (S2), Moderately Suitable (S3), Marginally Suitable (N1), and Permanently Not Suitable (N2), enabling the identification of spatial variability in enset suitability and supporting subsequent multi-criteria evaluation and weighted overlay analysis. The analysis evaluated criteria such as soil properties (type, depth, organic carbon content, pH, and texture), topographic situation (slope and elevation), climate variables (rainfall and temperature), and LULC. The integrated analysis revealed that enset cultivation is highly favorable across most of the study area, with 57.72% classified as highly suitable (S1), 36.89% as moderately suitable (S2), 0.16% as marginally suitable (S3), and 5.23% as currently not suitable (N1), while no areas were identified as permanently unsuitable (N2). Overall, the results highlight the strong natural potential of the Hadiya Zone for enset cultivation, although localized constraints related to soil fertility, water availability, and slope conditions may require targeted management interventions.},
}

Ethiopia
*Geographic Information Systems
*Crops, Agricultural/growth & development
*Agriculture/methods
Soil/chemistry
*Decision Support Techniques
*Conservation of Natural Resources

@article {pmid37766241,
year = {2023},
author = {Ritsch, M and Cassman, NA and Saghaei, S and Marz, M},
title = {Navigating the Landscape: A Comprehensive Review of Current Virus Databases.},
journal = {Viruses},
volume = {15},
number = {9},
pages = {},
pmid = {37766241},
issn = {1999-4915},
support = {NFDI 28/1//Deutsche Forschungsgemeinschaft/ ; CRC 1076//Deutsche Forschungsgemeinschaft/ ; EXC 2051//Deutsche Forschungsgemeinschaft/ ; 5575/10-9 TMWBDG//Ministry for Economics, Sciences and Digital Society of Thuringia (TMWWDG)/ ; 955974//EU Horizon/ ; },
mesh = {*Viruses/genetics/classification ; Genome, Viral ; *Databases, Genetic ; Humans ; *Databases, Factual ; Computational Biology/methods ; Metadata ; },
abstract = {Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.},
}

*Viruses/genetics/classification
Genome, Viral
*Databases, Genetic
Humans
*Databases, Factual
Computational Biology/methods
Metadata

@article {pmid41800995,
year = {2026},
author = {Reitz, ZL and Pourmohsenin, B and Susman, M and Thomsen, E and Roth, D and Butler, A and Ziemert, N and Medema, M},
title = {Automated genome mining predicts structural diversity and taxonomic distribution of peptide metallophores across bacteria.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.109154},
pmid = {41800995},
issn = {2050-084X},
support = {948770-DECIPHER/ERC_/European Research Council/International ; CHE-2108596//National Science Foundation/ ; H2020-FNR-11-2020//HORIZON EUROPE Framework Programme/ ; TTU09.716//Deutsches Zentrum für Infektionsforschung/ ; },
mesh = {*Bacteria/genetics/metabolism/classification ; *Genome, Bacterial ; *Peptides/chemistry/metabolism ; Algorithms ; *Metals/metabolism ; Multigene Family ; },
abstract = {Microbial competition for trace metals shapes their communities and interactions with humans and plants. Many bacteria scavenge trace metals with metallophores, small molecules that chelate environmental metal ions. Metallophore production may be predicted by genome mining, where genomes are scanned for homologs of known biosynthetic gene clusters (BGCs). However, accurately detecting non-ribosomal peptide (NRP) metallophore biosynthesis requires expert manual inspection, stymieing large-scale investigations. Here, we introduce automated identification of NRP metallophore BGCs through a comprehensive algorithm, implemented in antiSMASH, that detects chelator biosynthesis genes with 97% precision and 78% recall against manual curation. We showcase the utility of the detection algorithm by experimentally characterizing metallophores from several taxa. High-throughput NRP metallophore BGC detection enabled metallophore detection across 69,929 genomes spanning the bacterial kingdom. We predict that 25% of all bacterial non-ribosomal peptide synthetases encode metallophore production and that significant chemical diversity remains undiscovered. A reconstructed evolutionary history of NRP metallophores supports that some chelating groups may predate the Great Oxygenation Event. The inclusion of NRP metallophore detection in antiSMASH will aid non-expert researchers and continue to facilitate large-scale investigations into metallophore biology.},
}

*Bacteria/genetics/metabolism/classification
*Genome, Bacterial
*Peptides/chemistry/metabolism
Algorithms
*Metals/metabolism
Multigene Family

@article {pmid41799266,
year = {2026},
author = {Huang, JY and Weng, SF and Yang, ZS and Tung, YW and Wang, WH and Assavalapsakul, W and Thitithanyanont, A and Chao, DY and Lin, CY and Chen, YH and Wang, SF},
title = {A Large Dengue Outbreak in Taiwan, 2023: Driven by Imported Cases, Serotype Cocirculation, and Climate Variability.},
journal = {Open forum infectious diseases},
volume = {13},
number = {3},
pages = {ofag070},
pmid = {41799266},
issn = {2328-8957},
abstract = {BACKGROUND: Taiwan, a region traditionally considered non-endemic for dengue, experienced an unexpected and large-scale outbreak in 2023. We investigated the multifactorial drivers of this outbreak, including cross-border viral importation, serotype cocirculation, vector ecology, and climate variability.

METHODS: We analyzed national dengue surveillance data (2013-2023), meteorological records, and Breteau Index (BI) values, alongside molecular serotyping and whole-genome sequencing of clinical isolates. Time-lagged Poisson regression was used to identify predictors of indigenous dengue transmission in Kaohsiung and Tainan. Full-genome comparisons were conducted between 2023 strains and historical epidemic isolates.

RESULTS: A total of 26 706 laboratory-confirmed cases were reported, primarily in Tainan (80.7%) and Kaohsiung (11.9%). Real-time RT-PCR identified cocirculating DENV-1 and DENV-2 strains. Phylogenetic analysis confirmed the 2023 DENV-1 and DENV-2 strains were genetically linked to contemporary strains from Southeast Asian countries. Whole-genome sequencing identified several nonsynonymous mutations in the NS2A, NS3, and NS5 regions when compared with historical outbreak isolates. Time-lagged regression showed that imported cases, precipitation, and the BI were associated with incidence in univariate models. In Kaohsiung, the best-fitting multivariable model included the BI, but temperature and precipitation were the independent predictors. In Tainan, precipitation and, at longer lags, imported cases were more influential, while the BI lost significance after adjustment.

CONCLUSIONS: The 2023 dengue outbreak in Taiwan was driven by a complex interplay between viral introductions, climatic conditions, and vector dynamics. The differing transmission drivers observed between cities highlight the need for region-specific vector surveillance, climate-informed early warning systems, and sustained genomic monitoring to prevent future re-emergence of dengue in this non-endemic setting.},
}

@article {pmid41797873,
year = {2025},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Gorse Wanderer, Brachmia blandella (Fabricius, 1798) (Lepidoptera: Gelechiidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {551},
pmid = {41797873},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Brachmia blandella (Gorse Wanderer, Gorse Crest; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence has a total length of 498.99 megabases. Most of the assembly (96.45%) is scaffolded into 31 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.62 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41797871,
year = {2025},
author = {Sivess, L and Broad, GR and Holt, S and Boyes, D and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Pale Tussock moth, Calliteara pudibunda (Linnaeus, 1758) (Lepidoptera: Erebidae).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {587},
pmid = {41797871},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Calliteara pudibunda (Pale Tussock; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence has a total length of 1 035.55 megabases. Most of the assembly (99.83%) is scaffolded into 88 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled, with a length of 16.72 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.},
}

@article {pmid41795600,
year = {2026},
author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Wei, K and Tahir, M and Zhong, J},
title = {Multi-Omics Reveals Phenethyl Acetate and Its Producer Lactiplantibacillus plantarum as Key Drivers of Enhanced Palatability in Alfalfa Silage.},
journal = {Microbial biotechnology},
volume = {19},
number = {3},
pages = {e70332},
pmid = {41795600},
issn = {1751-7915},
support = {32201467//National Natural Science Foundation of China/ ; XDA26040201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025KJHZ0041//Science and Technology Program of the Inner Mongolia Autonomous Region/ ; },
mesh = {*Medicago sativa/microbiology/chemistry/metabolism ; *Silage/microbiology/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Taste ; *Acetates/metabolism ; Amino Acids/analysis/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Lactobacillaceae/metabolism ; Multiomics ; },
abstract = {High-quality silage enhances palatability and feed intake; however, the effects of co-fermentation with flavouring agents and lactic acid bacteria (LAB) on its flavour quality, core microbiota, and taste-active amino acids remain unclear. This study investigated the effects of fermentation using Lactiplantibacillus plantarum (LP) alone or in combination with phenethyl acetate (LPP) on the flavour profile of alfalfa silage and its subsequent influence on feed intake. Both LP and LPP significantly improved fermentation quality versus control (CK), with markedly higher feed intake-LP > CK and LPP > LP. Key flavour compounds, including dimethyl trisulfide, 4-ethylphenol and β-damascenone, were significantly increased in the LP alone group. Contrarily, essential taste-related amino acids including aspartic acid, alanine, proline, histidine, isoleucine, and valine were decreased, except for arginine. These metabolic shifts collectively contributed to enhanced feed intake. The addition of LPP increased phenylethyl alcohol, benzyl alcohol and hexanal, and decreased arginine, contributing to enhanced palatability. Aryl alcohol dehydrogenase, proline aminopeptidase, histidine dehydrogenase, and branched-chain amino acid transaminase from LP played a crucial role in the formation of phenylethyl alcohol, proline, histidine and isoleucine during fermentation. These results provide insights into how LAB and flavouring agents jointly regulate flavour development in high-quality alfalfa silage.},
}

*Medicago sativa/microbiology/chemistry/metabolism
*Silage/microbiology/analysis
Fermentation
*Flavoring Agents/metabolism
Taste
*Acetates/metabolism
Amino Acids/analysis/metabolism
*Lactiplantibacillus plantarum/metabolism
*Lactobacillaceae/metabolism
Multiomics

@article {pmid41793007,
year = {2026},
author = {Evans, LM and Arehart, CH and Gibson, RA and Bowman, GI and Gignoux, CR},
title = {A simple approach for multiple observations improves power to detect genetic effects and genomic prediction accuracy.},
journal = {HGG advances},
volume = {},
number = {},
pages = {100586},
doi = {10.1016/j.xhgg.2026.100586},
pmid = {41793007},
issn = {2666-2477},
abstract = {Many datasets, including widely used biobanks, have more than one observation of numerous phenotypes for at least a portion of their sample. The majority of GWAS utilize only a single observation per individual, even when more than one observation may be available, and apply a standard model in which the additive allelic effect being estimated is assumed to be constant across the age or time range in the sample. Here, we test a set of simple approaches to utilize multiple observations per individual, under this same assumption, to characterize effects on GWAS power, SNP-heritability, gene set enrichment, and polygenic prediction. We find that utilizing the mean or median of the available observations rather than a single observation improves power to detect associated loci and enriched gene sets and yields higher out-of-sample polygenic score prediction accuracy. Despite growing biobanks, many deeply phenotyped samples are relatively small but have multiple observations. While explicitly modeling age- or time-dependent genetic effects can add nuance to genetic studies and estimates, most GWAS apply a standard, additive-only model; a simple approach of using the mean or median can improve power by reducing "noise" in the phenotype, utilize standard, optimized software, and be particularly impactful for smaller samples, including samples of diverse genetic ancestry currently existing in widely used biobanks such as the UK Biobank and HRS.},
}

@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth & development ; Metagenomics/methods ; *Microbial Interactions ; Microbial Consortia/genetics ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}

*Vitamin B 12/metabolism/biosynthesis/genetics
*Mesorhizobium/genetics/metabolism
*Synechococcus/genetics/metabolism/growth & development
Metagenomics/methods
*Microbial Interactions
Microbial Consortia/genetics
Transcriptome
Gene Expression Profiling
Multiomics

@article {pmid41788053,
year = {2026},
author = {Lind, BM and Cobo-Simón, I and Myles, M and Barrett, G and Grau, E and Ramnath, R and Savitsky, V and Wegrzyn, JL},
title = {CartograPlant: Bridging genomic, phenotypic, and environmental data to advance plant resilience and eco-evolutionary insight.},
journal = {Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1093/genetics/iyag060},
pmid = {41788053},
issn = {1943-2631},
abstract = {Climate change is threatening plant health and productivity at all spatial scales, and these impacts are further compounded by the rising incidence of invasive pests and pathogens. Effectively addressing these challenges requires a comprehensive understanding of plant demography as well as the mechanisms and drivers of adaptation. Achieving this understanding requires the integration of physiological, ecological, and genetic datasets. However, such integration is often hindered by disconnected data sources, inconsistent metadata standards, and limited tools to link, analyze, and visualize multi-dimensional datasets in a unified framework. Addressing these hurdles is critical to advancing the understanding of species responses to environmental change and developing informed strategies for conservation, restoration, and adaptive management. CartograPlant (https://cartograplant.org) is a web-based interactive application which facilitates the visualization and analysis of genotypic, phenotypic, and environmental data, as well as associated metadata, from georeferenced individuals. Developed as a Tripal module, CartograPlant addresses a critical gap in biological data integration by enabling users to explore complex eco-evolutionary patterns across space and time. Recent updates have expanded its data sources, improved interoperability, and introduced NextFlow pipelines alongside new tools for the integration and analysis of these data. CartograPlant offers a scaleable, flexible, and continually-updated platform for researchers, conservationists, land managers, and plant breeders to better understand and mitigate the impacts of global change on plant biodiversity, accelerate resilience in breeding programs, and inform data-driven decisions in agriculture and ecosystem management.},
}

@article {pmid41785207,
year = {2026},
author = {Zhou, T and Wang, J and Zhao, Y and Sheng, Y},
title = {Land use change and ecological sensitivity in the Qingdao West Coast new area: A 30-year analysis and future scenario simulation.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0339986},
pmid = {41785207},
issn = {1932-6203},
mesh = {China ; *Conservation of Natural Resources ; Urbanization/trends ; *Ecosystem ; Sustainable Development/trends ; Humans ; Computer Simulation ; Geographic Information Systems ; },
abstract = {This study aims to reveal the long-term ecological evolution in the Qingdao West Coast New Area (QWCNA) and predict future trends to support its sustainable development. Firstly, it employed GIS-based land use dynamic indices and transfer matrix analyses to assess land use changes from 1990-2020. Secondly, this study assessed ecological sensitivity (1990-2020) using an Analytic Hierarchy Process (AHP) weighted 7-factor system covering the natural environment, land cover, and accessibility. Thirdly, the Patch-Generating Land Use Simulation (PLUS) model predicted 2030 land use under Natural Development (ND), Urban Development (UD), and Ecological Protection (EP) scenarios, which were subsequently used to evaluate future ecological sensitivity patterns. The main results indicate that a drastic land use transformation occurred between 1990 and 2020, marked by a significant expansion of construction land and forestland. This expansion primarily displaced cultivated land, grassland, water bodies, and unused land, driven by rapid urbanization. Furthermore, spatially distinct ecological sensitivity patterns evolved; lower sensitivity areas increased alongside urban expansion, while higher sensitivity zones (High and Extremely High), concentrated around the Xiaozhu, Dazhu, and Cangma-Tiejue Mts, expanded notably. The expansion of these higher sensitivity zones suggests potential environmental improvement attributed to enhanced conservation efforts. Future simulations show that the EP scenario best aligns with sustainability goals, maximizing the extent of High and Extremely High sensitivity areas by 2030 compared to the ND and UD scenarios.},
}

China
*Conservation of Natural Resources
Urbanization/trends
*Ecosystem
Sustainable Development/trends
Humans
Computer Simulation
Geographic Information Systems

@article {pmid41634835,
year = {2026},
author = {Vayena, E and Ataman, M and Hatzimanikatis, V},
title = {In silico analysis and comparison of the metabolic capabilities of different organisms by reducing metabolic complexity.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41634835},
issn = {2049-2618},
support = {200021_188623//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metabolic Networks and Pathways ; Computer Simulation ; *Saccharomyces cerevisiae/metabolism/genetics ; *Escherichia coli/metabolism/genetics ; Animals ; Bees/microbiology ; *Computational Biology/methods ; Algorithms ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Understanding how metabolic capabilities diverge across microbial species is essential for deciphering community function, ecological interactions, and the design of synthetic microbiomes. Despite shared core pathways, microbial phenotypes can differ markedly due to evolutionary adaptations and metabolic specialization. Genome-scale metabolic models (GEMs) provide a systems-level framework to explore these differences; however, their complexity hinders direct comparison.

RESULTS: We introduce NIS (Neidhardt-Ingraham-Schaechter), a computational workflow that integrates the redGEM, lumpGEM, and redGEMX algorithms to systematically reduce genome-scale models into biologically interpretable modules. This approach enables direct, quantitative comparison of fueling pathways, biomass biosynthetic routes, and environmental exchange processes while retaining essential metabolic information. We first demonstrate the utility of NIS by analyzing Escherichia coli and Saccharomyces cerevisiae, which revealed both conserved and divergent strategies in central metabolism, biosynthetic cost, and substrate utilization. We then applied NIS to the core honeybee gut microbiome, uncovering distinct metabolic traits, functional redundancy, and complementarity that help explain auxotrophy, cross-feeding interactions, and microbial coexistence.

CONCLUSIONS: NIS provides an automated, scalable, and reproducible framework for dissecting microbial metabolic networks beyond gene content or taxonomy. By linking metabolism to ecological function, NIS offers new opportunities to interpret microbial community dynamics and to support the rational design of microbiomes in health, agriculture, and environmental applications. Video Abstract.},
}

*Metabolic Networks and Pathways
Computer Simulation
*Saccharomyces cerevisiae/metabolism/genetics
*Escherichia coli/metabolism/genetics
Animals
Bees/microbiology
*Computational Biology/methods
Algorithms
Gastrointestinal Microbiome

@article {pmid41634548,
year = {2026},
author = {Ringeval, A and Modica, MV and Kantor, Y and Tenorio, MJ and Galindo, JCG and Puillandre, N and Farhat, S},
title = {Multi-omics characterization of toxin expression and producing organs in the predatory gastropods Monoplex corrugatus and Stramonita haemastoma.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41634548},
issn = {1471-2164},
mesh = {Animals ; *Gastropoda/genetics/metabolism ; Proteomics/methods ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {BACKGROUND: The exploration of toxin diversity is crucial for understanding the evolutionary adaptation of venomous taxa. Despite being active venomous predators, neogastropods are largely understudied beyond Conidae. This study targets two predatory gastropods, Monoplex corrugatus and Stramonita haemastoma, aiming to characterize their toxin-producing tissues, evaluate the diversity and function of their toxins, and compare gene expression profiles across tissues. Specimens of both species were dissected to isolate multiple replicates of secretory glands and other tissues. Transcriptomic data were complemented by shotgun proteomics for S. haemastoma and used to identify putative toxin genes using the DeTox pipeline. Differentially expressed genes were identified and putative toxins were manually annotated.

RESULTS: The study identified 2,565 and 1,777 putative toxins in S. haemastoma and M. corrugatus, respectively. Salivary glands were the major toxin-producing organ in both species, with additional toxin expression in mid-esophageal and accessory salivary glands. Manual annotation confidently identified 115 -S. haemastoma- and 143 -M. corrugatus- venom proteins, highlighting significant interspecies and inter-tissue differences. Functional categorization revealed the presence of enzymatic and peptide toxins, as well as venom-processing proteins, with M. corrugatus showing expression in non-secretory tissues. Despite their phylogenetic distance, shared orthologs were identified between the two species, namely for venom-processing proteins like calglandulin and disulfide isomerases, suggesting conserved functions. Toxins unique to each species analyzed, including echotoxins and plancitoxins in M. corrugatus, indicate lineage-specific venom adaptations. Proteomic validation supported transcriptomic predictions in S. haemastoma.

CONCLUSIONS: These findings underscore the value of multi-omics approaches for toxin discovery and for investigating the complexity of gastropod venom evolution and expand our understanding of how venom systems evolve and diversify in marine snails, highlighting both shared and unique toxin strategies that may reflect different ecological adaptations.},
}

Animals
*Gastropoda/genetics/metabolism
Proteomics/methods
Transcriptome
Gene Expression Profiling
Multiomics

@article {pmid41548390,
year = {2026},
author = {Xuan, F and Zhang, X and Hu, J and Li, X and Chen, Y and Zhang, A and Wang, R and Ren, Q and Wu, T and Guan, W and Cheng, Y and Zhou, J and Liu, R},
title = {Multi-omics dissection of large-size formation in Eriocheir sinensis: Insights from RNA, metabolite profiling, and ceRNA regulatory networks.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {58},
number = {},
pages = {101750},
doi = {10.1016/j.cbd.2026.101750},
pmid = {41548390},
issn = {1878-0407},
mesh = {Animals ; *Brachyura/genetics/metabolism/growth & development ; *Gene Regulatory Networks ; *Transcriptome ; *Body Size ; Metabolomics ; *Metabolome ; MicroRNAs/genetics ; Multiomics ; RNA, Competitive Endogenous ; },
abstract = {Eriocheir sinensis (Chinese mitten crab) is a key economic species in China's freshwater aquaculture industry. Individual body size is a critical trait that determines both market price and production profitability. Large-sized crabs exhibit substantial commercial advantages; however, the underlying molecular mechanisms regulating size formation remain poorly understood. In this study, we conducted an integrative multi-omics analysis combining whole-transcriptome data (mRNA, miRNA, and lncRNA) and untargeted metabolomics across two aquaculture cohorts (cohort2023 and cohort2024). Our results revealed a systemic downregulation of glycolysis, the tricarboxylic acid (TCA) cycle, fatty acid oxidation, and glycerol metabolism in large-sized crabs, suggesting a "low consumption-high storage" metabolic strategy. In contrast, pathways related to organismal development, exoskeleton reconstruction, steroid hormone biosynthesis, and nutrient absorption were significantly upregulated, indicating enhanced growth potential and nutrient assimilation efficiency. ceRNA network modeling and cis-acting lncRNA analysis identified multiple core regulatory genes (e.g., PTGS1, TPI1, POR) as targets of complex non-coding RNA interactions involved in body size regulation. Enzyme activity assays for key rate-limiting steps in carbohydrate and lipid catabolism, along with extensive qPCR validation, further corroborated the transcriptomic findings. Taken together, our study provides the first comprehensive multi-omics perspective on the molecular basis of body size differentiation in E. sinensis, proposing a tripartite mechanism involving suppressed catabolism, stimulated growth and morphogenesis, and improved nutrient acquisition. These findings offer theoretical insight into crustacean growth regulation and provide molecular targets to support selective breeding of high-value, large-sized mitten crab strains.},
}

Animals
*Brachyura/genetics/metabolism/growth & development
*Gene Regulatory Networks
*Transcriptome
*Body Size
Metabolomics
*Metabolome
MicroRNAs/genetics
Multiomics
RNA, Competitive Endogenous

@article {pmid41349461,
year = {2026},
author = {Qin, F and Liu, F and Cao, Q and Wei, Z and Gao, H and Zheng, W and Ke, Z and Xiong, Y and Luo, H and Wu, R and Wang, Z and Ye, H},
title = {A multi-omics atlas of testicular development in Leiocassis longirostris: dynamic regulation of spermatogenesis.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {58},
number = {},
pages = {101708},
doi = {10.1016/j.cbd.2025.101708},
pmid = {41349461},
issn = {1878-0407},
mesh = {Male ; Animals ; *Spermatogenesis ; *Testis/growth & development/metabolism ; *Catfishes/growth & development/genetics/metabolism ; *Fish Proteins/genetics/metabolism ; *Transcriptome ; Proteomics ; Multiomics ; },
abstract = {The Chinese longsnout catfish (Leiocassis longirostris) is a commercially valuable freshwater species in China. We elucidated molecular mechanisms underlying testicular development of L. longirostris across five stages (stages I to V) through integrated transcriptomic and proteomic analyses, which is crucial for enhancing its sperm quality and efficient reproduction. Enrichment analyses identified several key pathways as essential for testicular development, including TGF-β signaling, Wnt signaling, ECM-receptor interaction, ferroptosis, cell cycle regulation, and ubiquitin-mediated proteolysis. Gene Ontology (GO) enrichment highlighted core biological processes such as germ cell proliferation, differentiation, meiotic progression, and spermatogenesis regulation involved in development. Notably, qPCR validation showed peak expression levels of wnt7a, pax6, and kiss1r at distinct spermatogenic phases (p < 0.01), suggesting their potential as temporal biomarkers for identification of development stages. Furthermore, protein-protein interaction (PPI) analyses revealed C-type lysozyme (LysC) as a potential regulatory factor, with peak expression at stages I and III, possibly linking testicular immunity and reproductive processes. These findings elucidate the molecular mechanisms of testicular development and provide insights for developing efficient artificial breeding strategies for L. longirostris.},
}

Male
Animals
*Spermatogenesis
*Testis/growth & development/metabolism
*Catfishes/growth & development/genetics/metabolism
*Fish Proteins/genetics/metabolism
*Transcriptome
Proteomics
Multiomics

@article {pmid41787133,
year = {2026},
author = {Katzke, J and Hita Garcia, F and Lösel, PD and Azuma, F and Faragó, T and Aibekova, L and Casadei-Ferreira, A and Gautam, S and Richter, A and Toulkeridou, E and Bremer, S and Hamann, E and Hein, J and Odar, J and Sarkar, C and Zuber, M and Boomsma, JJ and Feitosa, RM and Schrader, L and Zhang, G and Csősz, S and Dong, M and Evangelista, O and Fischer, G and Fisher, BL and Florez-Fernandez, JA and , and García, F and Gómez, K and Grasso, DA and de Greef, S and Guénard, B and Hawkes, PG and Johnson, RA and Keller, RA and Larsen, RS and Linksvayer, TA and Liu, C and Matte, A and Ogasawara, M and Ran, H and Rodriguez, J and Schifani, E and Schultz, TR and Shik, JZ and Sosa-Calvo, J and Tong, C and Tozetto, L and Yoon, S and Yoshimura, M and Zhao, J and Baumbach, T and Economo, EP and van de Kamp, T},
title = {High-throughput phenomics of global ant biodiversity.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {41787133},
issn = {1548-7105},
support = {21K06326//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22KJ3077//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 24K01785//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; IC 180100008//Department of Education and Training | Australian Research Council (ARC)/ ; K 147781//Ministry of Science, Technology and Innovation | Conselho Nacional de Desenvolvimento Científico e Tecnológico (National Council for Scientific and Technological Development)/ ; 502787686//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DEB-1932467//National Science Foundation (NSF)/ ; IOS-2128304//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; DEB 1927161//National Science Foundation (NSF)/ ; ECF 137/2020//Environment and Conservation Fund (ECF)/ ; UIDB/00329/2020//NOVA | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; 05K2022//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 05K2019//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {The big data era in biology is underway, but the study of organismal form has been slow to capitalize on advances in imaging and computation. Imaging approaches can digitize whole organisms, but low throughput has limited the effort to document morphological diversity. Here, within the open science initiative 'Antscan', we applied high-throughput synchrotron X-ray microtomography to capture phenotypes across a diverse and ecologically dominant insect group: ants. At https://www.antscan.info , we provide 2,193 whole-body three-dimensional ant datasets from 212 genera and 792 species to broadly cover the ant phylogeny with a global scope, also pairing phenomic data with genome sequencing projects. Scans acquired with standardized parameters facilitate automated analysis, and free access to data can broaden the audience and incentivize methods development. Antscan presents a scalable approach to create libraries of diverse anatomies, heralding an era of studies on the evolution, structure and function of organismal phenotypes.},
}

@article {pmid41786578,
year = {2026},
author = {Xu, N and Zhang, Z and Xu, H and Yao, J and Lu, H and Cai, W and Ou, Y and Luan, H and Gong, P and Tu, W and Li, Q},
title = {Multifaceted assessment of recent saltwater intrusion along China's coasts.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2026.02.021},
pmid = {41786578},
issn = {2095-9281},
}

@article {pmid41779789,
year = {2026},
author = {Gonzalez, A and August, T and Bailey, S and Bobiwash, K and Boersch-Supan, PH and Burgess, ND and Daru, BH and Elphick, CS and Freckleton, RP and Frick, WF and Hughes, AC and Isaac, NJB and Jones, JPG and Lambertini, M and Mac Aodha, O and Madhavapeddy, A and Milner-Gulland, EJ and Purvis, A and Salafsky, N and Sutherland, WJ and Tanshi, I and Vijay, V and Woodard, SH and Williams, DR},
title = {From data to decisions: Toward a Biodiversity Monitoring Standards Framework.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {10},
pages = {e2519347123},
doi = {10.1073/pnas.2519347123},
pmid = {41779789},
issn = {1091-6490},
support = {101133983//European Union/ ; },
mesh = {*Biodiversity ; *Conservation of Natural Resources/methods ; *Environmental Monitoring/methods/standards ; Decision Making ; },
abstract = {Achieving the goals of the Kunming-Montreal Global Biodiversity Framework (GBF) requires monitoring systems that can transform heterogeneous observations into consistent, decision-relevant knowledge. Yet current biodiversity data are fragmented, uneven in quality, and seldom comparable across space or time. Existing standards such as Darwin Core, Findable, Accessible, Interoperable, and Reusable (FAIR) and Collective Benefit, Authority to Control, Responsibility, and Ethics (CARE) principles provide important foundations, but they do not connect the full chain from field observation to policy reporting. We introduce the Biodiversity Monitoring Standards Framework (BMSF)-a unifying architecture that links ethical principles, standardized data collection, accredited analytical workflows, and transparent reporting into a single auditable "chain of evidence." The framework's novelty lies in its tiered and federated design, enabling national agencies, Indigenous knowledge holders, local communities, and private-sector actors to operate under shared principles while maintaining data sovereignty. By integrating Essential Variables, accredited analytical methods, and open-source implementation pathways, the BMSF allows locally generated data to be aggregated into credible, comparable indicators aligned with GBF targets. Concrete application, such as a national forest-connectivity assessment, demonstrates how the BMSF improves reproducibility, transparency, and policy relevance relative to existing approaches. Implemented generally, this framework would convert fragmented monitoring efforts into a coordinated, scalable system capable of tracking and guiding collective progress toward halting and reversing biodiversity loss.},
}

*Biodiversity
*Conservation of Natural Resources/methods
*Environmental Monitoring/methods/standards
Decision Making

@article {pmid41762296,
year = {2026},
author = {Vohra, R and Mishra, P},
title = {Sustainable mapping identification of municipal solid waste disposal zones using RS-GIS-basedMCDA techniques: a case study in Darjeeling, West Bengal.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {3},
pages = {},
pmid = {41762296},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; India ; *Refuse Disposal/methods ; *Solid Waste/statistics & numerical data/analysis ; *Remote Sensing Technology ; Cities ; Decision Support Techniques ; },
abstract = {Demographic expansion together with fast-paced urbanization within hilly terrain of ecologically fragile areas such as Darjeeling in West Bengal complicated the process of managing municipal solid waste (MSW). A study develops a comprehensive geospatial method which combines remote sensing (RS) and geographic information systems (GIS) with multi-criteria decision analysis (MCDA) to locate sustainable zones for municipal solid waste disposal. The study examines the Darjeeling Municipality area alongside its 2-km surrounding zone which demonstrates steep topography and density as well as ecological risks. A spatial decision support system (SDSS) is developed using a multi-criteria RS-GIS framework to determine the suitable areas for municipal solid waste disposal site suitability (MSWDSS). The framework standardizes geospatial and urban planning criteria through quantitative evaluation of slope, elevation, land use/land cover, and areas around roads, water bodies, and settlements which are weighted using analytic hierarchy process (AHP). The weighted linear combination (WLC) technique is used to compute a composite suitability index, ensuring proportional influence from each criterion after normalization. For proximity-sensitive factors, a Gaussian decay function is applied to model nonlinear reductions in suitability near sensitive infrastructure. The parameters were weighted using AHP based on their influence on landfill site suitability, with land value (0.184), distance to settlement (0.135), and distance to road (0.123) receiving the highest weights. These reflect the prioritization of economic feasibility, public health, and operational efficiency. Spatial data layers were generated, reclassified, and overlaid in a GIS environment to produce a composite suitability map. The final map classified land into three suitability zones: high, moderate, and low, highlighting that high suitability zones are located in the southern and southwestern parts of Darjeeling Municipality, characterized by low population density, low land value, greater distance from sensitive sites, gentle slopes, and poor access to existing waste services. The composite MSWDSS index is classified using natural breaks (Jenks) into three suitability categories: high (≥ 0.66), moderate (0.33-0.65), and low (≤ 0.32), to support informed site selection under constrained urban conditions. Findings reveal that only a limited portion of the study area meets the environmental and infrastructural criteria for landfill development, owing to Darjeeling's challenging topography and dense urban fabric. Nevertheless, the model successfully identifies zones with optimal accessibility, minimal ecological disruption, and reduced risks of leachate contamination and landslides. The findings show that the analysis produced the best results when applied to the study area, optimizing the balance between environmental, infrastructural, and economic factors.},
}

*Geographic Information Systems
*Environmental Monitoring/methods
India
*Refuse Disposal/methods
*Solid Waste/statistics & numerical data/analysis
*Remote Sensing Technology
Cities
Decision Support Techniques

@article {pmid41760678,
year = {2026},
author = {Leiva, FP and Molina-Venegas, R and Alter, K and Freire, CA and Hendriks, AJ and Hermaniuk, A and Serre-Fredj, L and Shokri, M and Czarnoleski, M and Mark, FC},
title = {ErythroCite: a database on red blood cell size of fishes.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41760678},
issn = {2052-4463},
mesh = {Animals ; *Fishes/blood ; *Erythrocytes/cytology ; Female ; Male ; *Cell Size ; *Databases, Factual ; },
abstract = {Size is a fundamental trait in biology, and cell size plays a key role in cellular functions, influencing physiological adaptations and evolutionary processes in living organisms. For decades, scientists have been fascinated by the considerable variation in cell sizes among animals, yet systematic efforts to compile such data have been scarce. To address this gap, we employed a systematic map approach to create ErythroCite, an open-source database of fish erythrocyte sizes. This comprehensive resource encompasses 1,764 records from 660 species among four major lineages: Actinopterygii, Chondrichthyes, Dipnoi, and Cyclostomata. Our findings reveal a remarkable 414-fold range in cell volume, with most studies on bony fishes and limited data on juveniles and earlier life stages. Life stage and sex were infrequently reported, but available data showed equal representation of adult of females and males. ErythroCite offers valuable insights for studies in macroecology, macrophysiology, comparative physiology, evolutionary biology and cell biology. We anticipate this resource will facilitate comparative approaches and meta-analyses, globally driving further exploration of erythrocyte diversity and function in fish.},
}

Animals
*Fishes/blood
*Erythrocytes/cytology
Female
Male
*Cell Size
*Databases, Factual

@article {pmid41755684,
year = {2026},
author = {Li, H and Li, S},
title = {Computer-Assisted Performance-Based Assessment for Mental Health: A Scoping Review.},
journal = {PsyCh journal},
volume = {15},
number = {2},
pages = {e70086},
pmid = {41755684},
issn = {2046-0260},
support = {2021YFC3340800//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Adolescent ; *Mental Health ; *Mental Disorders/diagnosis ; *Diagnosis, Computer-Assisted/methods ; Reproducibility of Results ; },
abstract = {Adolescent mental health is foundational to personal development, yet it faces escalating challenges globally. While traditional assessment methods lack objectivity and ecological validity, integrating computer-assisted technology (CAT) into performance-based assessments (PBAs) offers a promising pathway. This review, following the PRISMA-ScR reporting standard, analyzed 89 articles (2015-2025) to map the assessed components, CAT applications, and scenario diversity in mental health PBAs. Analysis revealed a research emphasis on mental disorders, with critical domains for adolescent development remaining significantly understudied. CATs significantly enhanced PBAs through data analysis, data acquisition, scenario creation, and tool digitization. PBA scenarios are diverse, demonstrating the adaptability of PBAs for multidimensional mental health assessment. Prioritizing the design of PBAs for social-emotional and adaptive assessment is critical for the early identification of adolescent mental health issues. Furthermore, advancing predictive analytics and leveraging large language models for feedback generation are promising ways to unlock CAT's potential in enhancing PBAs. Importantly, integrating and adapting scenarios from validated scales by CATs into PBAs could further enhance assessment typicality and reliability.},
}

Humans
Adolescent
*Mental Health
*Mental Disorders/diagnosis
*Diagnosis, Computer-Assisted/methods
Reproducibility of Results

@article {pmid41741096,
year = {2026},
author = {Weingarden, H and Holstein, V and Jonathan, GK and Armey, M and Onnela, JP and Wilhelm, S},
title = {Low-Burden Detection of Clinical Worsening in Body Dysmorphic Disorder Using Smartphone Sensor and Demographic Data.},
journal = {Behavior therapy},
volume = {57},
number = {2},
pages = {220-233},
pmid = {41741096},
issn = {1878-1888},
support = {K23 MH119372/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; *Smartphone ; Female ; Male ; *Body Dysmorphic Disorders/diagnosis/psychology ; Adult ; *Ecological Momentary Assessment ; Young Adult ; Machine Learning ; Adolescent ; Suicidal Ideation ; Middle Aged ; Accelerometry ; Geographic Information Systems ; Wearable Electronic Devices ; },
abstract = {Body dysmorphic disorder (BDD) is characterized by distressing preoccupations with perceived appearance flaws, leading to functional impairment and suicidal ideation (SI). Traditional approaches for monitoring clinical deterioration in BDD include self-reports and clinician assessments, which can miss acute changes in risk due to infrequent administration and recall biases. Alternatively, real-time monitoring via smartphones and wearable devices can enable low-burden early detection of deterioration, identifying intervention opportunities before someone's condition critically worsens. This study tests the feasibility of using smartphone sensor and demographic data to predict daily clinical acuity. Eighty-two participants with BDD completed ecological momentary assessments (EMA) over 28 days, reporting levels of SI, BDD-related avoidance, and time spent on BDD-related concerns. Smartphone sensor data were collected for 3 months that overlapped with EMA. Machine learning models were trained to predict same-day levels of SI, avoidance, and time spent on BDD using the Global Positioning System (GPS), accelerometer, and demographic data. We evaluated model performance using mean absolute error, Pearson and Spearman correlations, and permutation tests. Random forest (RF) models using time and random split validation outperformed dummy regressor models across outcomes (maximum SI, mean SI, maximum avoidance, mean avoidance, time spent on BDD-related behaviors). Pearson correlations for RF models showed strong predictive performance for BDD-related time (r = .74-.75) and mean and max SI (r = .70-.73). Mean and max avoidance was moderately well predicted (r = .56-.62). Step count and demographic factors (e.g., education, living situation) were the most consistent and important features. This study provides initial evidence that smartphone sensor and demographic data can be used to monitor real-time clinical worsening in BDD, without burdening the patient. This work has potential for building just-in-time interventions that are delivered as deterioration onsets, to prevent its escalation. Future research should test these models in real-world datasets collected over longer periods and subsequently explore integration into interventions and clinical decision making. Trial Registration: ClinicalTrials.gov Identifier: NCT04254575.},
}

Humans
*Smartphone
Female
Male
*Body Dysmorphic Disorders/diagnosis/psychology
Adult
*Ecological Momentary Assessment
Young Adult
Machine Learning
Adolescent
Suicidal Ideation
Middle Aged
Accelerometry
Geographic Information Systems
Wearable Electronic Devices

@article {pmid41662977,
year = {2026},
author = {Kaya, C},
title = {Metabolomics-guided engineering of drought-resilient crops: Integrating multi-omics and AI for climate-smart agriculture.},
journal = {Plant science : an international journal of experimental plant biology},
volume = {365},
number = {},
pages = {113025},
doi = {10.1016/j.plantsci.2026.113025},
pmid = {41662977},
issn = {1873-2259},
mesh = {*Metabolomics/methods ; *Crops, Agricultural/genetics/metabolism/physiology ; *Droughts ; *Artificial Intelligence ; *Agriculture/methods ; Plant Breeding ; Gene Editing ; Stress, Physiological ; Multiomics ; },
abstract = {Drought stress is among the most critical threats to global food security, and its complex impact on plant physiology often exceeds the reach of traditional breeding approaches. Metabolomics has emerged as a transformative tool for dissecting drought responses, enabling dynamic, systems-level characterization of primary and secondary metabolites that mediate osmotic balance, redox homeostasis, and stress acclimation. Building on earlier reviews that primarily focused on stress-associated metabolites, this article emphasizes the integration of metabolomics with cutting-edge technologies, CRISPR-based genome editing, pathway engineering, synthetic biology, and artificial intelligence, to establish a translational framework for drought-resilient cropimprovement. Recent advances in analytical platforms, bioinformatics pipelines, and crop-specific case studies are critically examined to demonstrate how metabolomic signatures can be translated into predictive biomarkers and incorporated into breeding pipelines. In addition, emerging frontiers such as single-cell and spatial metabolomics, ecological metabolomics, and AI-driven predictive modeling are highlighted as promising directions for connecting laboratory discoveries with field-scale applications. By synthesizing technological and biological advances, this review outlines how metabolomics can evolve from a diagnostic tool into a predictive and prescriptive platform, positioning it as a key component of climate-smart agriculture and next-generation crop improvement.},
}

*Metabolomics/methods
*Crops, Agricultural/genetics/metabolism/physiology
*Droughts
*Artificial Intelligence
*Agriculture/methods
Plant Breeding
Gene Editing
Stress, Physiological
Multiomics

@article {pmid41662342,
year = {2026},
author = {Chen, J and Feng, Y and Zhang, Y and Gao, J and Ou, J and Wu, W and Li, C and Song, S and Tai, L and Rifat, MH and Akhter, D and Hu, J and Feng, P and Shen, XX and Pan, R},
title = {Structure-guided discovery of protein functions in plants.},
journal = {The Plant cell},
volume = {38},
number = {2},
pages = {},
doi = {10.1093/plcell/koag022},
pmid = {41662342},
issn = {1532-298X},
support = {32470287//National Natural Science Foundation of China/ ; 32500235//National Natural Science Foundation of China/ ; 32200231//National Natural Science Foundation of China/ ; R26C130007//Zhejiang Provincial Natural Science Foundation of China/ ; QN26C020005//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C020002//Zhejiang Provincial Natural Science Foundation of China/ ; 2025SZRJJ0918//Natural Science Foundation of Hangzhou/ ; 2024SZRYBC130003//Natural Science Foundation of Hangzhou/ ; 2022YFD1401600//National Key Research and Development/ ; 2024YFD1200401//National Key Research and Development/ ; 2024M762901//China Postdoctoral Science Foundation/ ; 2025T180747//China Postdoctoral Science Foundation/ ; 2025M782775//China Postdoctoral Science Foundation/ ; 2025M772587//China Postdoctoral Science Foundation/ ; },
mesh = {*Plant Proteins/metabolism/chemistry/genetics ; Databases, Protein ; Magnoliopsida/metabolism/genetics ; },
abstract = {Protein structure serves as a critical bridge between sequence and functional annotation, particularly in establishing functional links among distantly homologous proteins with low sequence similarities. However, systematic protein structure-based functional annotations have been lacking in plants, where functions for a significant portion of the proteomes are still elusive. In this study, we leveraged protein structural data from 17 angiosperms to uncover previously unannotated protein functions in plants. After structural clustering, we used the plant clusters to query the UniProtKB/Swiss-Prot database (the expertly curated component of UniProtKB), a repository of expertly curated and reliably annotated proteins, and identified structural matches for thousands of plant clusters that were undetectable by sequence-based BLAST searches. We further selected 120 clusters, which are highly reliable in structural quality and alignment and are well-conserved across plant species, and uncovered various protein functions that are potentially widely important in plants. Finally, we experimentally analyzed one plant cluster structurally resembling the yeast peroxisomal peroxin 8 (PEX8) protein and verified that plant PEX8-like proteins can functionally complement yeast pex8 mutants. Our findings highlight the power of structural comparison in uncovering protein functions in plants.},
}

*Plant Proteins/metabolism/chemistry/genetics
Databases, Protein
Magnoliopsida/metabolism/genetics

@article {pmid41643351,
year = {2026},
author = {Itzkovitch, A and Sulami, I and Efroni, RD and Shahar, M and Levy, O},
title = {From big data to small scales: Machine learning enhances microclimate model predictions.},
journal = {Journal of thermal biology},
volume = {136},
number = {},
pages = {104387},
doi = {10.1016/j.jtherbio.2026.104387},
pmid = {41643351},
issn = {0306-4565},
mesh = {*Machine Learning ; *Microclimate ; *Big Data ; *Climate Models ; Climate Change ; Ecosystem ; },
abstract = {Microclimates are critical for understanding how organisms interact with their environments, influencing behaviour, physiology, and species distributions. However, traditional physical heat-balance models for predicting ground temperatures in microhabitats often exhibit biases due to unaccounted environmental complexities and poorly constrained parameters. These limitations can hinder ecological research and conservation planning, particularly in the context of climate change. In this study, we demonstrate how high-resolution drone-based mapping and machine learning can improve the accuracy of microclimate models. Using drone imagery, we generated detailed environmental maps, including solar radiation, vegetation indices, and skyview factors, to parameterize a physical heat-balance model. Validation with thermal maps derived from drone-mounted infrared cameras revealed systematic errors in the physical model's predictions, including over- and underestimations under specific environmental conditions. To address these errors, we applied a random forest machine learning model to predict and correct biases in new prediction maps. Our results show that machine learning reduced mean absolute errors by over 30% and mean square errors by 50%, while consistently narrowing the range of prediction inaccuracies. Key factors driving biases, such as vegetation cover, solar radiation, and height above ground, were identified, offering valuable insights for improving physical models. The machine learning corrections not only improved accuracy but also highlighted parameters and processes that were previously underrepresented or oversimplified in traditional models. These findings illustrate the potential of machine learning to improve microclimate predictions. While our drone-based approach is most applicable to open, sparsely vegetated habitats, the principle of machine learning bias correction can be extended to other systems as well. Correcting microclimate models with machine learning and observational data provides ecologists and conservation practitioners with a powerful framework for generating more accurate microclimate estimates. Such improvements deepen our understanding of species' responses to climate change and support climate-resilient management strategies.},
}

*Machine Learning
*Microclimate
*Big Data
*Climate Models
Climate Change
Ecosystem

@article {pmid41620065,
year = {2026},
author = {Zhou, Y and Wang, Y and Si, P and Zhao, X and Kong, Q and Zhang, H},
title = {Naphthenic acid exposure disrupts mitochondrial function and locomotor behavior in marine medaka (Oryzias melastigma) via G protein-coupled receptor signaling: A multi-omics perspective.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123919},
doi = {10.1016/j.envres.2026.123919},
pmid = {41620065},
issn = {1096-0953},
mesh = {Animals ; *Oryzias/physiology ; *Water Pollutants, Chemical/toxicity ; *Receptors, G-Protein-Coupled/metabolism ; *Mitochondria/drug effects ; Signal Transduction/drug effects ; *Carboxylic Acids/toxicity ; *Locomotion/drug effects ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Naphthenic acids (NAs) are a class of toxic petroleum-derived carboxylic acids that are being increasingly detected in marine environments at ecologically concerning concentrations. However, the molecular initiating events underlying NA toxicity and the adaptive responses of marine organisms during prolonged exposure remain poorly defined. In this study, juvenile marine medaka (Oryzias melastigma) were exposed to environmentally relevant NA concentrations for up to 28 days. Multi-omics and molecular docking analyses indicated that the NAs interacted with G-protein coupled receptors (GPCRs) in marine medaka, disrupting mTOR and FoxO signaling and enhancing oxidative stress. Antioxidant depletion was associated with mitochondrial damage and apoptosis, leading to dysfunction. Combined with the disturbance of lipid metabolism (glycerophospholipids, ether lipids, and sphingolipids), this disrupted the energy supply and induced abnormal locomotor behavior. Notably, low-level NA exposure initially elicited stimulatory responses, which transitioned to inhibitory effects over time. This temporal shift likely results from the progressive accumulation of oxidative stress, ultimately amplifying the ecological risks associated with prolonged exposure. Overall, this study elucidates a previously uncharacterized receptor-mediated pathway underlying NA toxicity and establishes a quantitative framework for evaluating the long-term ecological risks posed by petrochemical pollutants. These findings provide mechanistic and predictive insights for assessing environmental health risks from chronic low-dose NA exposure in marine ecosystems.},
}

Animals
*Oryzias/physiology
*Water Pollutants, Chemical/toxicity
*Receptors, G-Protein-Coupled/metabolism
*Mitochondria/drug effects
Signal Transduction/drug effects
*Carboxylic Acids/toxicity
*Locomotion/drug effects
Oxidative Stress/drug effects
Multiomics

@article {pmid41580412,
year = {2026},
author = {Draisma, A and Loureiro, C and Louwen, NLL and Kautsar, SA and Navarro-Muñoz, JC and Doering, DT and Mouncey, NJ and Medema, MH},
title = {BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41580412},
issn = {2041-1723},
support = {OSF.23.1.044//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Multigene Family ; *Software ; Microbiota/genetics ; Databases, Genetic ; Cluster Analysis ; *Computational Biology/methods ; Metabolic Networks and Pathways/genetics ; },
abstract = {Microbial metabolic gene clusters encode the biosynthesis or catabolism of metabolites that facilitate ecological specialization, mediate microbiome interactions and constitute a major source of medicines and crop protection agents. Here, we present BiG-SCAPE and BiG-SLiCE 2.0, next-generation methods that facilitate scalable, accurate and interactive gene cluster analyses. BiG-SCAPE 2.0 updates its classification, alignment methods, and visualizations, enabling more accurate analysis, up to 8x faster runtimes and halved memory requirements. BiG-SLiCE 2.0 updates its distance metric, pHMM database, and classification logic, resulting in increased sensitivity nearing that of BiG-SCAPE. Analysis of 260,630 biosynthetic gene clusters from publicly available genomes reveals that both tools generate concurring estimates of gene cluster diversity, thus providing significantly extended methodological support for recent evidence indicating that the vast majority of natural product diversity remains unexplored. Together, these updates will facilitate global genome mining efforts for natural product discovery and microbiome analyses scalable with current data sizes.},
}

*Multigene Family
*Software
Microbiota/genetics
Databases, Genetic
Cluster Analysis
*Computational Biology/methods
Metabolic Networks and Pathways/genetics

@article {pmid41563008,
year = {2026},
author = {Karatzas, E and Beracochea, M and Baltoumas, FA and Aplakidou, E and Richardson, L and Fellows Yates, JA and Lundin, D and , and Buluç, A and Kyrpides, NC and Georgakopoulos-Soares, I and Pavlopoulos, GA and Finn, RD},
title = {nf-core/proteinfamilies: a scalable pipeline for the generation of protein families.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
pmid = {41563008},
issn = {2047-217X},
support = {//European Union/ ; DE-AC02-05CH11231//Hellenic Foundation for Research and Innovation/ ; },
mesh = {*Proteins/chemistry/genetics/classification ; *Software ; *Computational Biology/methods ; Databases, Protein ; Metagenomics/methods ; Sequence Alignment ; Molecular Sequence Annotation ; },
abstract = {The growth of metagenomics-derived amino acid sequence data has transformed our understanding of protein function, microbial diversity, and evolutionary relationships. However, the vast majority of these proteins remain functionally uncharacterized. Grouping the millions of such uncharacterized sequences with the few experimentally characterized ones allows the transfer of annotations, while the inspection of conserved residues with multiple sequence alignments can provide clues to function, even in the absence of existing functional information. To address the challenges associated with this data surge and the need to group sequences, we present a scalable, open-source, parametrizable Nextflow pipeline (nf-core/proteinfamilies) that generates nascent protein families or assigns new proteins to existing families. The computational benchmarks demonstrated that resource usage scales approximately linearly with input size, and the biological benchmarks showed that the generated protein families closely resemble manually curated families in widely used databases.},
}

*Proteins/chemistry/genetics/classification
*Software
*Computational Biology/methods
Databases, Protein
Metagenomics/methods
Sequence Alignment
Molecular Sequence Annotation

@article {pmid41547155,
year = {2026},
author = {Liu, X and Zhang, H and Su, T and Arshad, M and Gao, W and Zhang, S and Wu, J and Li, H},
title = {Multi-omics analysis reveals immune responses in tobacco leaves treated with polyethylene nanoparticles.},
journal = {Plant physiology and biochemistry : PPB},
volume = {231},
number = {},
pages = {111026},
doi = {10.1016/j.plaphy.2026.111026},
pmid = {41547155},
issn = {1873-2690},
mesh = {*Nicotiana/immunology/drug effects/metabolism/microbiology/genetics ; *Plant Leaves/immunology/drug effects/metabolism ; *Nanoparticles/chemistry ; *Polyethylene/pharmacology/chemistry ; Reactive Oxygen Species/metabolism ; *Plant Immunity/drug effects ; Gene Expression Regulation, Plant/drug effects ; Pseudomonas syringae ; Transcriptome/drug effects ; Plant Proteins/metabolism/genetics ; Proteome/metabolism ; Multiomics ; },
abstract = {As an emerging contaminant, nanoplastics (NPs) could enter plant tissues through roots and leaves, posing threats to plant growth. Majority of the earlier studies have focused on the toxic effects of NPs after their uptake and the potential non-toxicological biological impacts. We found that 20 nm polyethylene NPs (PE-NPs) could rapidly induce stomatal closure in tobacco leaves after 1 h of exposure, along with increased reactive oxygen species levels and up-regulated expression of pathogenesis-related genes. These responses were similar to those induced by pathogen-associated molecular patterns (PAMPs), as in case of response to pathogen recognition. Subsequent multi-omics integration analyses of transcriptome, proteome, metabolome, and phosphoproteome revealed convergent and divergent responses of tobacco leaves to PE-NPs and the tobacco pathogen Pseudomonas syringae pattern-triggered immunity (PTI) responses. Tobacco leaves responded to both elicitors in a similar manner at the transcriptome and proteome levels, exhibiting numerous similar PTI response patterns, but distinct at the metabolome levels. The differences might arise from elicitor-specific phosphorylation events during post-translational modification, which reshaped gene expression by modulating enzyme activity, leading to distinct metabolite profiles. Our multi-level regulatory network revealed the molecular framework by which NPs as abiotic stressors activated plant innate immunity, providing a novel perspective for understanding the ecological impacts of NPs.},
}

*Nicotiana/immunology/drug effects/metabolism/microbiology/genetics
*Plant Leaves/immunology/drug effects/metabolism
*Nanoparticles/chemistry
*Polyethylene/pharmacology/chemistry
Reactive Oxygen Species/metabolism
*Plant Immunity/drug effects
Gene Expression Regulation, Plant/drug effects
Pseudomonas syringae
Transcriptome/drug effects
Plant Proteins/metabolism/genetics
Proteome/metabolism
Multiomics

@article {pmid41528732,
year = {2026},
author = {Ivancevic, A and Sankovitz, M and Allen, H and Joyner, O and Chuong, EB and Ramsey, SD},
title = {Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.},
journal = {G3 (Bethesda, Md.)},
volume = {16},
number = {3},
pages = {},
pmid = {41528732},
issn = {2160-1836},
support = {//Study of Honey Bee Pest Diversity to Support Development of Emergency Response Plan/ ; //United States Department of Agriculture Animal Plant Health Inspection Service/ ; //National Geographic Wayfinder Award/ ; 2R35GM128822/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bees/genetics/classification ; *Genome, Insect ; Molecular Sequence Annotation ; *Whole Genome Sequencing ; Genomics/methods ; Computational Biology/methods ; },
abstract = {The Micrapis subgenus, which includes the black dwarf honey bee (Apis andreniformis) and the red dwarf honey bee (Apis florea), remains underrepresented in genomic studies despite its ecological significance. Here, we present high-quality de novo genome assemblies for both species, generated using a hybrid sequencing approach combining Oxford Nanopore Technologies long reads with Illumina short reads. The final assemblies are highly contiguous, with contig N50 values of 5.0 Mb (A. andreniformis) and 4.3 Mb (A. florea), representing a major improvement over the previously published A. florea genome. Genome completeness assessments indicate high quality, with BUSCO scores exceeding 98.5% using the Hymenoptera database and k-mer analyses supporting base-level accuracy. Repeat annotation revealed a relatively low repetitive sequence content (∼6%), consistent with other Apis species. Using RNA sequencing data, we annotated 12,189 genes for A. andreniformis and 12,207 genes for A. florea, with ∼98% completeness in predicted proteomes. These genome assemblies provide a valuable resource for comparative and functional genomic studies, with the potential to offer new insights into the genetic basis of dwarf honey bee adaptations.},
}

Animals
Bees/genetics/classification
*Genome, Insect
Molecular Sequence Annotation
*Whole Genome Sequencing
Genomics/methods
Computational Biology/methods

@article {pmid41455431,
year = {2026},
author = {Pazhamala, L and Pandey, M and Deveshwar, P and Ghatak, A and Weckwerth, W and Chaturvedi, P and Giri, J},
title = {Network-based multiomics and transgenic validation reveal that OsPHR3 modulates phosphate-carbon metabolic trade-offs during rice seed development.},
journal = {Plant physiology and biochemistry : PPB},
volume = {231},
number = {},
pages = {110981},
doi = {10.1016/j.plaphy.2025.110981},
pmid = {41455431},
issn = {1873-2690},
mesh = {*Oryza/metabolism/genetics/growth & development ; *Seeds/metabolism/growth & development/genetics ; *Phosphates/metabolism ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified/metabolism ; *Carbon/metabolism ; Gene Expression Regulation, Plant ; Phytic Acid/metabolism ; Starch/metabolism ; Multiomics ; },
abstract = {Phosphate (Pi) allocation during the grain-filling stage is a major determinant of crop yield, supporting macromolecule synthesis, energy metabolism, and nutrient storage. However, its storage as phytic acid (PA) reduces nutritional quality by chelating essential minerals. Despite its importance, a comprehensive understanding of the molecular mechanisms integrating Pi transport, carbohydrate metabolism, and PA biosynthesis during seed development remains incomplete. To address this gap, we investigated stage-specific phosphate regulatory networks in rice by integrating transcriptomic, proteomic, and metabolomic approaches. Temporal expression profiling and gene coexpression network analyses of phosphate regulators and transporter genes revealed their distinct roles during early and mid-grain filling stages. PHOSPHATE STARVATION RESPONSE 3 (OsPHR3) emerged as a central regulatory hub, coordinating the balance of Pi, sugar, starch and phytate, along with other metabolites. Network-based multiomics integration further identified 126 genes involved in nutrient storage and stress tolerance, with myo-inositol-1-phosphate synthase (OsMIPS1) and starch synthase 3 (OsSSIII) as key genes. CRISPR/Cas9-generated osphr3 knockout lines confirmed the critical role of OsPHR3 in regulating these target genes. Mutants exhibited significantly reduced seed starch, PA, and total phosphorus contents, while scanning electron microscopy revealed aberrant starch granule morphology. Loss-of-function of OsPHR3 lowered PA levels by 19.46-22.50 %, with moderate trade-offs in yield-related traits. Although, OsPHR3 is known to contribute to nitrogen and phosphorus homeostasis, our findings establish it as a key regulator orchestrating a stage-specific phosphate-carbon allocation during seed development. These insights provide key targets for refining nutrient partitioning to achieve increased yields, reduced phytic acid, and enhanced phosphorus use efficiency for agricultural sustainability.},
}

*Oryza/metabolism/genetics/growth & development
*Seeds/metabolism/growth & development/genetics
*Phosphates/metabolism
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified/metabolism
*Carbon/metabolism
Gene Expression Regulation, Plant
Phytic Acid/metabolism
Starch/metabolism
Multiomics

@article {pmid41242981,
year = {2026},
author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A},
title = {The fetal exposome and preterm birth: a systematic synthesis of environmental exposures and multi-omics evidence.},
journal = {Journal of perinatal medicine},
volume = {54},
number = {2},
pages = {391-407},
pmid = {41242981},
issn = {1619-3997},
mesh = {Humans ; Female ; Pregnancy ; *Premature Birth/etiology/epidemiology ; *Exposome ; *Environmental Exposure/adverse effects ; Infant, Newborn ; *Maternal Exposure/adverse effects ; Multiomics ; },
abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.

METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.

RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.

CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.},
}

Humans
Female
Pregnancy
*Premature Birth/etiology/epidemiology
*Exposome
*Environmental Exposure/adverse effects
Infant, Newborn
*Maternal Exposure/adverse effects
Multiomics

@article {pmid41215744,
year = {2026},
author = {Wei, Y and Lin, Z and Xie, Q and Gao, J and Jin, J and Li, J and Lu, C and Ye, G and Li, W and Huang, C and Yang, D and Liu, Q and Zhu, G and Yang, F},
title = {OrchidMD: An Integrated and User-Interactive Orchid Multi-Omics Database for Mining Genes and Biological Research.},
journal = {Plant biotechnology journal},
volume = {24},
number = {3},
pages = {1885-1897},
pmid = {41215744},
issn = {1467-7652},
support = {2023YFD2300904//National Key Research and Development Program of China/ ; CYZX202406//Guangdong Academy of Agricultural Sciences Project/ ; R2020PY-JX018//Guangdong Academy of Agricultural Sciences Project/ ; R2023PY-JG023//Guangdong Academy of Agricultural Sciences Project/ ; XTXM202201//Guangdong Academy of Agricultural Sciences Project/ ; XT202212//Guangdong Academy of Agricultural Sciences Project/ ; 2024B1212060012//Science and Technology Planning Project of Guangdong Province/ ; 2024CXTD12//Innovation Team of Modern Agriculture Industry Technology System in Guangdong Province/ ; 2024-NPY-00-035//Seed Industry Revitalization Project of the Special Fund for the Rural Revitalization Strategy of Guangdong Province/ ; 2024A1515013187//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011604//Guangdong Basic and Applied Basic Research Foundation/ ; 2025010//Ex Situ Conservation and Artificial Propagation of National Key Protected Orchids and Ferns/ ; R2021YJ-XD001//Special Foundation for Introduction of Scientific Talents of GDAAS/ ; //Modern Seed Industry Innovation Capability Enhancement Project of Guangdong Academy of Agricultural Sciences/ ; },
mesh = {*Orchidaceae/genetics/metabolism ; *Data Mining ; *Genomics/methods ; *Databases, Genetic ; Metabolomics ; Proteomics ; Phenomics ; Multiomics ; },
abstract = {The Orchidaceae family, with its unparalleled species diversity among angiosperms, is integral to ornamental, medicinal, cultural, and ecological value. Multi-omics techniques have proven invaluable for the identification of candidate genes and the advancement of functional genomics research. Nevertheless, the application of these technologies in Orchidaceae remains severely limited due to the lack of effective platforms that can integrate and analyze multi-omics data, especially in understanding the mechanisms underlying key traits such as distinctive floral morphology. In this study, we present OrchidMD, the Orchid Multi-omics Database (www.orchidcomics.com), a resource platform that integrates data from five omics layers: genomics, transcriptomics, proteomics, metabolomics, and phenomics, encompassing a total of 213 species. OrchidMD is equipped with 18 specialized statistical and analytical tools, and features a user-friendly interface that facilitates efficient gene mining, multi-omics data exploration, and integrative interactive analysis. A case study on the comprehensive identification of the pan-ARF gene family across Orchidaceae species demonstrates the effectiveness and convenience of OrchidMD. Furthermore, experimental validation further shows that transgenic overexpression of CsiARF04 promotes the differentiation and budding of orchid rhizomes. In addition, another case study using gene editing in orchids, CRISPR Design was employed to predict the CsiPDS target site in Cymbidium sinense. Effective editing was subsequently achieved via Agrobacterium-mediated delivery of the CRISPR/Cas9 vector into leaves. These results underscore OrchidMD's formidable capacity to discern candidate genes associated with salient traits and elucidate their regulatory mechanisms. Thus, OrchidMD serves as a pivotal platform advancing multi-dimensional biological research and functional genomics in orchids.},
}

*Orchidaceae/genetics/metabolism
*Data Mining
*Genomics/methods
*Databases, Genetic
Metabolomics
Proteomics
Phenomics
Multiomics

@article {pmid41726913,
year = {2026},
author = {Chalar, R and Khatri, N and Obeid, J and Downey, E and Song, JH and Xiao, Y and Samad, S and Chen, A and Resnick, A and Karbalaei, K and Allopenna, JJ and Mao, C and Clarke, C and Velazquez, F and Luberto, C and Chen, B and Canal, D and Hannun, Y and Damaghi, M},
title = {Metabolic plasticity of sphingolipids governs cancer cell fitness in acidic tumor ecosystems.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41726913},
issn = {2692-8205},
abstract = {Cancer cells must adapt to harsh tumor microenvironments, including acidic stress, to survive and thrive. Understanding how cancer cells achieve this adaptation can uncover new biomarkers and therapeutic strategies. In this study, we investigated the spatial metabolic phenotypic heterogeneity of breast cancer cells in acidic habitats using spatial multi-omics approaches on 3D spheroids. We found that cancer cells dynamically regulate sphingolipid metabolism to fine-tune their cell state to cope with acidic selection pressures. Cancer cells evolve mechanisms to deal with initially accumulating toxic ceramides but later adapt to it by rerouting SL metabolic pathways to eliminate them. Using advanced MALDI image analysis, and SL inhibitors on patient derived organoids, we demonstrated that cancer cells can switch between metabolic routes when key pathways are blocked, showcasing remarkable cell state plasticity. These insights highlight the potential to target metabolic plasticity as a novel therapeutic strategy to disrupt cancer adaptation and evolution, offering new avenues for cancer treatment.},
}

@article {pmid41779788,
year = {2026},
author = {Sutherland, WJ and Burgess, ND and Edwards, SV and Jones, JPG and Soltis, PS and Tilman, D and Allen, JM and Andrianandrasana, HT and Armour, CJ and August, T and Bawa, KS and Bailey, S and Birch, T and Boersch-Supan, PH and Cavender-Bares, J and Blaxter, M and Chaplin-Kramer, R and Daru, BH and De Palma, A and Eisenberg, C and Elphick, CS and Freckleton, RP and Frick, WF and Gonzalez, A and Goetz, SJ and Greenspoon, L and Grozingeree, CM and Hankins, DL and Hazell, J and Isaac, NJB and Lambertini, M and Lewin, HA and Mac Aodha, O and Madhavapeddy, A and Milner-Gulland, EJ and Milo, R and O'Dwyer, J and Purvis, A and Salafsky, N and Tallis, H and Tanshi, I and Vijay, V and Wikelski, M and Williams, DR and Woodard, SH and Robinson, GE},
title = {Nine changes needed to deliver a radical transformation in biodiversity measurement.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {10},
pages = {e2519345123},
doi = {10.1073/pnas.2519345123},
pmid = {41779788},
issn = {1091-6490},
support = {101133983//More4nature/ ; },
abstract = {Biodiversity is declining in many parts of the world. Biological diversity measurement and monitoring are fundamental to the assessment of the causes and consequences of environmental changes, identification of key areas for the protection of biodiversity or ecosystem services, determining the effectiveness of actions, and the creation of decision-support tools critical to maintaining a sustainable planet. Biodiversity measurement is rapidly changing due to advances in citizen science, image recognition, acoustic monitoring, environmental DNA, genomics, remote sensing, and AI. In this perspective, we outline the exciting opportunities these developments offer but also consider the challenges. Our key recommendations are to 1) Capitalize on the ability of novel technology to integrate data sources 2) agree to standard methods for data collection 3) ensure new technologies are calibrated with existing data; 4) fill data gaps by using emerging technologies and increasing capacity, especially in the tropics; 5) create living safeguarded databases of trusted information to reduce the risk of poisoning by AI hallucinated, or false, information; 6) ensure data generation is valued; 7) ensure respectful incorporation of Indigenous Knowledge; 8) ensure measurements enable the quantification of effectiveness of actions, and 9) increase the resilience of global datasets to technical and societal change. Radical new collaborations are needed between computer scientists, engineers, molecular biologists, data scientists, field ecologists, citizen scientists, Indigenous peoples, policymakers, and local communities to create the rigorous, resilient, accessible biodiversity information systems required to underpin policies and practices that ensure the maintenance and restoration of ecological systems.},
}

@article {pmid41779521,
year = {2026},
author = {Laguna, GGC and Gusmão, ALF and Gusmão, ABF and Fernandes, JSG and Fonseca, YS and Azevedo, KMR},
title = {Silent wounds: an epidemiological analysis of self-inflicted injuries among youths in Brazil (2013-2023).},
journal = {Cadernos de saude publica},
volume = {42},
number = {},
pages = {e00062525},
doi = {10.1590/0102-311XEN062525},
pmid = {41779521},
issn = {1678-4464},
abstract = {This study aimed to describe the epidemiological profile of self-inflicted injuries among children and adolescents in Brazil over the past decade (2013-2023). This ecological study had a nationwide coverage and was based on data from the Brazilian Health Informatics Department (DATASUS). Descriptive and inferential statistical analysis were applied (t-test, ANOVA, Tukey, and Friedman), with normality assessment (Shapiro-Wilk), using Jamovi software. From 2013 to 2023, 18,382 hospitalizations and 261 deaths due to self-inflicted injuries were recorded among children and adolescents in Brazil, with a total hospital cost of approximately BRL 10 million. The Southeast accounted for the highest number of hospitalizations (55.45%) and deaths (60.1%), while the North reported the lowest figures. The most affected age group was 15-19 years. Hospitalizations were more frequent among females, whereas deaths predominated among males, with a significant impact on the Black population. During the study period, hospitalizations increased by 44.28% and deaths by 26.31%, with the highest hospital costs occurring in 2022 and 2023. These findings reveal significant regional and demographic disparities and underscore the need for targeted prevention strategies and specific public health policies.},
}

@article {pmid41779489,
year = {2026},
author = {Moura, PH and Carvalho, LDG and Godoy, PH and Salis, LHA and Paez, MS and Alves, MB and Maia, LFPG and Santos, RLD and Silva, NASE},
title = {Impact of PM2.5 Air Pollution on Mortality from Circulatory System Diseases in the Neighborhoods of the City of Rio de Janeiro (2000-2019).},
journal = {Arquivos brasileiros de cardiologia},
volume = {123},
number = {1},
pages = {e20250459},
doi = {10.36660/abc.20250459},
pmid = {41779489},
issn = {1678-4170},
abstract = {BACKGROUND: Air pollution by fine particulate matter with an aerodynamic diameter ≤ 2.5 μm (PM2.5) is the main environmental risk factor associated with diseases of the circulatory system (DCS), ischemic heart disease (IHD), and cerebrovascular diseases (CBVD).

OBJECTIVE: To estimate mortality rates from DCS, IHD, and CBVD (2000-2019) among residents of the 164 neighborhoods of Rio de Janeiro, according to PM2.5 levels.

METHODS: This retrospective ecological study used georeferenced satellite data classified into three PM2.5 levels and mortality records from the Department of Information and Informatics of the Unified Health System for DCS, IHD, and CBVD among individuals of both sexes aged ≥ 20 years from 2000 to 2019. Age-adjusted mortality rates per 1,000 inhabitants were calculated, and comparative statistical analyses were performed by sex, PM2.5 level, and age group (5% significance).

RESULTS: Approximately 91% of the 4.7 million residents (≥ 20 years) live in areas with high or extreme PM2.5 pollution. Deaths occurred up to 3.4 years earlier among men living in highly polluted areas compared with those in moderately polluted areas. The highest DCS mortality rates were observed in neighborhoods with high and extreme pollution (female = 3.9 ± 1.7; 95% CI = 3.5-4.2; male = 4.6 ± 2.1; 95% CI = 4.1-4.9), particularly in individuals aged ≥ 70 years. Significant associations were found between mortality rates and pollution levels for DCS (p = 0.019), IHD (p = 0.025), and CBVD (p = 0.002) in the 50-69-year age group when comparing moderately and extremely polluted areas. Intermediate/high social vulnerability was identified in 71% of neighborhoods, with an increasing socioenvironmental gradient linking higher vulnerability to higher PM2.5 concentrations (R = 0.354; p = 0.001).

CONCLUSION: Mean PM2.5 concentrations in the neighborhoods of Rio de Janeiro exceeded the World Health Organization's recommended standard by a factor of four. Mortality from DCS is significantly higher and occurs earlier in areas with high or extreme levels of pollution.},
}

@article {pmid41388798,
year = {2026},
author = {Haahtela, T and O'Mahony, L and Traidl-Hoffmann, C and Akdis, M and Ceylan, O and Chaslaridis, P and Damialis, A and Del Giacco, S and Lauerma, A and Nadeau, KC and Paciência, I and Pali-Schöll, I and Palomares, O and Renz, H and Schwarze, J and Urrutia-Pereira, M and Venter, C and Vercelli, D and Winders, T and Akdis, CA and Jutel, M and Agache, I},
title = {EAACI Guidelines on the Importance of Green Space in Urban Environments for Allergy and Asthma Prevention.},
journal = {Allergy},
volume = {81},
number = {3},
pages = {635-650},
pmid = {41388798},
issn = {1398-9995},
support = {43205//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {The allergy and asthma epidemic in urban societies following World War II is mostly caused by changes in the environment, diet and lifestyle. Disconnection of urban populations from the wider environment has reduced the protective factors building up immunological resilience. The European Academy of Allergy and Clinical Immunology (EAACI) guidelines on greenness impact on allergy and asthma follow the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach and provide eight recommendations encouraging greenness exposure to support immune health. Controlled follow-up studies are still scarce, and the strength of evidence is generally low or moderate at best. For primary prevention of allergy and asthma, most of the evidence indicates beneficial effects. Exposure is also useful for secondary prevention. Asthma patients may feel better and need less medication by combining green space exposure with physical activity. During the high-pollen season, effective seasonal medication is necessary for patients with pollen allergy. In urban planning, implementing appropriate green infrastructure and easy access to green space promotes immune health and reduces risks of air pollution and heatwaves. These EAACI guidelines are the first recommendations highlighting the importance of urban green spaces on immune health and call for prioritising innovative research in this field.},
}

@article {pmid41775999,
year = {2026},
author = {Steindorff, AS and Cai, FM and Ding, M and Jiang, S and Atanasova, L and Baker, SE and Barbosa-Filho, JR and Bayram Akcapinar, G and Brown, DW and Chaverri, P and Chen, P and Chenthamara, K and Daum, C and Drula, E and Dubey, M and Brandström Durling, M and Flatschacher, D and Ebner, T and Emri, T and Gao, R and Georg, RC and Henrissat, B and Hermosa, R and Herrera-Estrella, A and Hinterdobler, W and Kainz, P and Karlsson, M and Kredics, L and Kubicek, CP and Kuo, A and LaButti, K and Lipzen, A and Lorito, M and Mach, RL and Manganiello, G and Marik, T and Martinez-Reyes, N and Mayrhofer-Reinhartshuber, M and Miskei, M and Moisan, MC and Mondo, S and Monte, E and Ng, V and Pang, G and Pangilinan, J and Peng, M and Piombo, E and Pócsi, I and Rahimi, MJ and Reddy, SK and Riley, R and Sarrocco, S and Schmal, M and Schmoll, M and Szűcs, A and Woo, SL and Yarden, O and Zeilinger, S and Zimmermann, C and Shelest, E and Tsang, A and Berka, R and de Vries, RP and Grigoriev, IV and Druzhinina, IS},
title = {Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41775999},
issn = {2058-5276},
support = {32470020//National Natural Science Foundation of China (National Science Foundation of China)/ ; DEB-1638976//National Science Foundation (NSF)/ ; DEB-1019972//NSF | National Science Board (NSB)/ ; },
abstract = {Trichoderma fungi support sustainable agriculture by suppressing plant diseases and improving crop performance. However, emerging pathogenicity of Trichoderma warrants further ecological and genetic characterization. Here we used machine learning to correlate genomic data from 37 Trichoderma strains with over 140 phenotypic traits, spanning metabolic versatility, biotic interactions, stress tolerance and reproductive strategies. We determined Trichoderma to be an ancient, genetically cohesive and physiologically diverse genus with spores capable of germination in water and dispersal via air and water droplets. Metabolic preferences indicate universal adaptation to mycoparasitism and to niches like arboreal microbial mats, alongside broader saprotrophic versatility. Our analyses are consistent with character displacement among close relatives and convergent evolution in distant lineages, with both processes shaping ecological plasticity and traits including dispersal modes, terrestrialization or endophytism. Our findings reveal that while some Trichoderma species show traits of biosafety concern, its vast ecophysiological diversity enables the development of safe, targeted bioeffectors.},
}

@article {pmid41768530,
year = {2026},
author = {Ross-Adelman, M and Aalbers, G and Matcham, F and Leightley, D and Oetzmann, C and Carr, E and Siddi, S and Haro, JM and Annas, P and Dalby, M and Narayan, VA and Hotopf, M and Myin-Germeys, I and Lamers, F and Penninx, BWJH and , },
title = {Sleep, Steps, and Screens: Between- and within-person effects of digital markers of daily life behaviors on smartphone-based assessments of cognitive functioning in depression.},
journal = {Neuroscience applied},
volume = {5},
number = {},
pages = {106985},
pmid = {41768530},
issn = {2772-4085},
abstract = {Cognitive impairment represents a core feature of major depressive disorder (MDD), often persisting after mood symptoms remit and not addressed by usual antidepressant treatments. Despite its relevance, cognition is typically assessed with infrequent tests in clinical settings, overlooking its contextual nature. Smartphones and wearables enable ecologically valid, repeated measurements of cognition and daily life behaviors that may impact it. We examined whether sleep duration, step count, and smartphone screen time are associated with cognitive functioning in MDD. We conducted secondary analyses of RADAR-MDD, a multicenter study following individuals with recurrent MDD. Cognitive functioning - self-reported and performance-based - was assessed with the THINC-it® app. Sleep duration and step count were measured with Fitbit devices, and screen time with the RADAR-Base app. Cognitive assessments (outcomes) were linked to behavioral measures (predictors) from the day of and the day preceding each assessment. Two-level multilevel models estimated between-person (differences in participant means) and within-person (deviations from participant means) effects. The sample included 502 participants, further subdivided by behavior-cognitive outcome pair. For performance-based cognitive assessments, positive associations at the between-person level were found for step count (β = 0.104, SE = 0.031, p < 0.001) and screen time (β = 0.075, SE = 0.036, p = 0.038), and sleep duration showed a quadratic negative effect (β = -0.080, SE = 0.018, p < 0.001). No within-person effects were detected. For self-reported cognitive functioning, step count showed positive associations both between (β = 0.161, SE = 0.037, p < 0.001) and within persons (β = 0.027, SE = 0.010, p = 0.005), while screen time was negatively associated within persons (β = -0.033, SE = 0.011, p = 0.002). Our findings illustrate that smartphones and wearables can collect meaningful daily life data of MDD patients that can be used to support cognitive health. Step count emerges as a promising behavioral target as it is simple to track and is correlated with better cognitive outcomes.},
}

@article {pmid41768099,
year = {2023},
author = {Boyes, D and Phillips, D and , and , and , and , and , and , },
title = {The genome sequence of the Dusky Thorn moth, Ennomos fuscantarius (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {505},
doi = {10.12688/wellcomeopenres.20174.2},
pmid = {41768099},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ennomos fuscantarius (the Dusky Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 444.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.49 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,173 protein coding genes.},
}

@article {pmid41765545,
year = {2026},
author = {Xiong, H and Yin, Y and Cui, X and Dai, W and Dong, J and Wang, X and Duan, G},
title = {Impacts of coal mining on heavy metal concentration and microbial community composition in surrounding soils.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {465-475},
doi = {10.1016/j.jes.2025.05.060},
pmid = {41765545},
issn = {1001-0742},
abstract = {Coal mining activities have been demonstrated to result in substantial environmental contamination, posing severe risks to surrounding soil ecosystems. However, the interaction between microbial community structure and environmental factors in coal mining areas remains poorly understood. In this study, we evaluated the health status of soils and the effects of heavy metals on microbial community structure in coal mining areas through comprehensive soil health assessments and sequencing. Our findings revealed that soils impacted by mining activities exhibited low soil health index values, with health grades ranging from moderate to poor. Active biomarkers including Gemmatimonadota (phylum), Patescibacteria (phylum), and Saccharimonadia were highly enriched in mine soils, with some developing metal tolerance. Additionally, potential pathogenic bacteria, including MND1, Bacillus, and Pannonibacter, and potential pathogenic fungi including Fusarium and Alternaria, showed significantly higher abundance in these soils. Heavy metal concentrations, particularly Cu and As, were strongly correlated with the distribution of certain bacterial genera, alongside variations in soil physicochemical properties, including C/N ratios and organic matter content. These findings demonstrate complex relationships among heavy metal pollution, soil properties, and microbial communities, underlining the potential risks posed by mining activities to soil health and agricultural productivity in affected regions.},
}

@article {pmid41764794,
year = {2026},
author = {Wang, Z and Zhang, G and Lu, X and Lei, R and Zhou, W and Tian, Y and Lu, Y and Tu, L and Li, S},
title = {Transforming mine dump waste soil into biogeo-composites with vegetation growth regulation function through bio-mediated treatment.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141630},
doi = {10.1016/j.jhazmat.2026.141630},
pmid = {41764794},
issn = {1873-3336},
abstract = {Valorization of mine waste soils into sustainable materials provides both ecological protection and recycling benefits. This study develops a calcium lignosulfonate (CLS)-enzyme-induced calcium carbonate precipitation (EICP)-driven biogeo-composite that simultaneously enhances mechanical stability, regulates hydraulic behavior, and promotes vegetation growth. Laboratory tests demonstrated that CLS-EICP treatment increased shear strength of soils through cohesion enhancement driven by rigid CaCO3 bonding and ductile CLS bridging. Hydraulic conductivity reduced by two orders of magnitude and slaking resistance significantly enhanced. Microstructural analyses confirmed a dense organic-inorganic hybrid network formation, enabling a transition from surface to volumetric cementation and promoting structural densification. Field trials further validated these findings, as biogeo-composite-treated slopes resisted gully erosion, delayed pore water pressure build-up, and maintained overall stability while supporting uniform vegetation growth. These results highlight the dual role of CLS-EICP composites in slope reinforcement and eco-functional regulation, offering a scalable pathway for the valorization of waste soils.},
}

@article {pmid41764240,
year = {2026},
author = {Alice, S and Pierangela, P and Giuseppe, B and Fabio, P and Stefania, P},
title = {Ecosystem structure influences human health outcomes as the basis for green prescriptions.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40752-8},
pmid = {41764240},
issn = {2045-2322},
abstract = {The role of Nature [**][**] in supporting human life, health, and well-being has been recognized and appreciated since ancient times, and has become a topic of scientific investigation with early studies dating back several decades. In recent years, this field has gained renewed attention and methodological refinement, driven by interdisciplinary frameworks and advances in environmental psychology, ecology, and health sciences, including new ecosystem-based approaches that highlight the deep human dependence on Nature for both mental and physical health. Among Nature-based Interventions that aim at exposing people to the natural environment, Green Prescriptions (GRx) represent a promising strategy to address human health challenges in ways that can also support environmental sustainability, in line with the Planetary Health framework. However, significant gaps remain in our understanding of the specific ecological factors that influence health outcomes during therapeutic activities in natural settings; in particular, it remains unclear how ecosystem structure and functions modulate health responses in individuals. This nine-month pilot study examined the therapeutic efficacy of GRx within a Mediterranean woodland ecosystem, to assess if and how variations in ecosystem structure influence health outcomes in individuals with complex chronic conditions. Using a novel aggregated index to characterize four distinct woodland patches, we identified a gradient in structural complexity where greater ecosystem functionality was consistently associated with greater alleviation of psychological and physical symptoms. Notably, health outcomes were independent of weather conditions and participants' baseline connectedness to Nature, whereas temporal dynamics and the presence of peaks in the productivity of some species influenced both perceptions and physical responses. This underscores the intrinsic role of ecosystem properties and dynamic functions in modulating human health responses, while also suggesting the potential presence of a complex set of signals pervading complex ecosystems that is worth further exploration. The results demonstrated cumulative health benefits, including significant reductions in medication use over time, particularly among individuals with respiratory challenges and chronic pain. Furthermore, participants showed improved environmental awareness and behavior, embracing the interconnectedness principle, which is integral to effective environmental conservation. This study highlights the potential of well-functioning ecosystems to serve as co-effectors in healthcare interventions, advancing the goals of Planetary Health while reinforcing the importance of preserving ecological integrity. (**In this paper, "Nature" is written with a capital "N" to indicate the living biosphere and the abiotic matrices (soil, air, and water) in which life is embedded, including the ecological processes they sustain. This capitalization reflects the scientific perspective of Nature not merely as a passive backdrop, but as an active ecological system that interacts and influences human health. It also avoids confusion with "nature" as the intrinsic quality of a phenomenon**).},
}

@article {pmid41762592,
year = {2026},
author = {Salarzaei, S and Shiri, F and Ahmadi, S},
title = {A global Quasi-SMILES model based on the Monte Carlo algorithm for assessing the multi-organism aquatic ecotoxicity of personal care products.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119948},
doi = {10.1016/j.ecoenv.2026.119948},
pmid = {41762592},
issn = {1090-2414},
abstract = {Personal care products (PCPs) are widely used for external applications on the body, and their increased consumption has raised concerns about their potential environmental impact, particularly in aquatic ecosystems. Evaluating the aquatic ecotoxicity of PCPs is essential, but the process is a long and difficult task. Thus, it is crucial to employ tools for rapid screening. The quantitative structure-activity relationship (QSAR) approach can leverage existing data to identify potentially hazardous PCPs quickly. This study uses QSAR models to assess the aquatic ecotoxicity of 159 PCPs across three organisms' algae, crustaceans, and fish providing a broader ecological perspective than traditional methods, which typically focus on a single organism. A QSAR model was implemented using CORAL software, which utilizes the SMILES format to predict aquatic toxicity. However, traditional SMILES do not incorporate experimental context, limiting prediction accuracy. To address this, the Quasi-SMILES method extends the traditional SMILES notation by incorporating experimental conditions related to three key organisms of the aquatic trophic level algae (Pseudokirchneriella subcapitata), crustacean (Daphnia magna), and fish (Pimephales promelas) thus enabling more accurate predictions of chemical behavior under diverse environmental conditions. Using random data splitting and multiple objective functions, 40 models were developed based on the Monte Carlo method. The model that combined the Ideal Correlation Index (IIC) and the Correlation Intensity Index (CII) as dual objective functions achieved the best predictive performance for split 4, with rm[2] = 0.7396, R[2]= 0.7757, and Q[2] = 0.7509 for validation set highlighting the effectiveness of multi-objective optimization strategies.},
}

@article {pmid41760830,
year = {2026},
author = {Abraham, AJ and Duvall, ES and Leese, C and Abraham, K and le Roux, E and Riond, B and Ortmann, S and Terranova, M and Leese, G and Bailey, MA and Clauss, M},
title = {Preliminary evidence of extrarenal sodium storage in a large mammal: implications for comparative physiology and hypertension research : Running: Sodium storage in cattle.},
journal = {Pflugers Archiv : European journal of physiology},
volume = {478},
number = {3},
pages = {},
pmid = {41760830},
issn = {1432-2013},
abstract = {Under conditions of dietary sodium (Na[+]) excess, the kidneys may fail to adequately excrete Na[+], potentially compromising blood pressure homeostasis. Body tissues, such as skin, can offer sites of short-term extrarenal Na[+] storage and previous research has shown that this can help guard against hypertension in small mammals (e.g., rodents). Large mammals have relatively greater Na[+] storage potential, but whether extrarenal Na[+] storage occurs for this group is unknown. Here, we report preliminary evidence of extrarenal Na[+] storage in cattle. We provided a large pulse-dose of NaCl to four cattle (body mass: ~720 kg) and measured excretion of Na[+] and potassium (K[+]) in urine and faeces for a period of 7-days. Following NaCl administration, Na[+] excretion spiked in both urine and faeces for ~ 48 h before returning to baseline measurements. After ~ 96 h, however, Na[+] excretion increased again; a consistent physiological phenomenon across all individuals studied. We did not observe a pattern in urinary K[+] excretion, indicating that the mechanism of Na[+] storage does not appear to involve exchange for K[+]. However, faecal K[+] excretion was reciprocal to that of Na[+], presumably reflecting exchange of Na[+]/K[+] across the walls of the large intestine. We infer that during the initial period of Na[+] stress, short-term extrarenal Na[+] storage occurred and the stored Na[+] was later released only when the body had returned to Na[+] homeostasis. Additional experiments are required to understand how patterns of Na[+] regulation changes across body sizes and the specific body compartments involved. Cattle may be a useful model system for examining the impact of high Na[+] intake in mammals larger than humans.},
}

@article {pmid41758169,
year = {2026},
author = {Sun, Y and Jaiswal, A and Kargarandehkordi, A and Slade, C and Benzo, RM and Phillips, KT and Washington, P},
title = {Barriers to Designing Inclusive Ecological Momentary Assessment and Wearable Data Collection Protocols for AI-Driven Substance Use Monitoring in Hawai'i.},
journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing},
volume = {31},
number = {},
pages = {566-579},
doi = {10.1142/9789819824755_0041},
pmid = {41758169},
issn = {2335-6936},
abstract = {Ecological momentary assessment (EMA) and wearable sensors offer unprecedented opportunities to capture the dynamics of substance use through real-time, high-resolution behavioral and physiological data. These data streams are increasingly used to train AI/ML models for digital phenotyping and predictive intervention, raising critical questions about fairness, bias, and inclusivity in model development. However, the adoption of these technologies, or the lack thereof, among diverse and historically marginalized groups raises questions and challenges of equity, cultural relevance, and participant trust. In this study, we conducted a four-week observational study with adults in Hawai.i where we combined continuous Fitbit monitoring and daily EMA surveys to document substance use patterns and cravings. Through semi-structured interviews and grounded theory analysis, we identified six primary barriers to study participation and adherence: (1) disruptions to daily routines, (2) physical and psychosocial discomfort associated with wearing the Fitbit device, (3) concerns about aesthetic compatibility and professional appearance, (4) phonerelated issues, (5) challenges related to substance use and cravings, and (6) socially sensitive contexts. We also highlight participant-identified facilitators, such as the value of participant-driven scheduling, motivational feedback, and contextually adaptive protocols. Drawing on these collective findings, we propose a set of design guidelines aimed at advancing the inclusivity, engagement, and fairness of wearable-based EMA research.},
}

@article {pmid41755163,
year = {2026},
author = {Hu, Q and Hou, R and Kou, Y and Wang, P and Liu, Z and Li, H and Liu, W and Wang, X and Yi, S and Zhang, F and Zhou, Z and Zhang, M and Li, X and Wu, Q},
title = {Investigating Mining-Induced Surface Subsidence in Mountainous Areas Using Integrated InSAR and GNSS Monitoring.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {4},
pages = {},
pmid = {41755163},
issn = {1424-8220},
support = {42277478//National Natural Science Foundation of China/ ; U21A20109//National Natural Science Foundation of China/ ; 52274165//National Natural Science Foundation of China/ ; 2024YFC3212200//National Key Research and Development Program of China/ ; 242300421041//Henan Science Foundation for Distinguished Young Scholars of China/ ; 25IRTSTHN008//Henan Provincial University Science and Technology Innovation Team Support Program/ ; 241111321100//Henan Key Research and Development Program of China/ ; },
abstract = {Leveraging the complementary advantages of InSAR and GNSS, this study proposes a refined method for monitoring mining-induced surface subsidence by integrating both technologies. The method begins with calculating the time-series cumulative subsidence basin from InSAR. Subsequently, a constraint condition is established to identify large-gradient deformations, thereby distinguishing the subsidence edge from the subsidence center. For the subsidence edge with minor deformation, the InSAR results are retained. For the large-gradient subsidence center, the subsidence basin around the mining panel is reconstructed by integrating InSAR and GNSS models. Continuous surface deformation information in a geographic coordinate system is then obtained through spatial interpolation, ultimately yielding comprehensive surface subsidence results across the mining area. Taking a mining area in Shanxi Province as the study region, the feasibility and accuracy of the proposed method were validated using 35 SAR images acquired between April 2016 and September 2017, along with leveling measurement data from the mining panel. The maximum surface subsidence rate of the settlement basin obtained from the solution is -186.68 mm/year, and the maximum surface subsidence amount is 248 mm. Compared with the InSAR monitoring results, the root mean square error of the data collaborative monitoring is reduced by 96.8%, and it is reduced by 64.4% compared with the GNSS probability integral method. The results demonstrate that the proposed method can achieve subsidence results consistent with the actual situation. Its monitoring capability is significantly superior to that of using either InSAR or GNSS alone, effectively compensating for the limitations inherent in each individual technology when applied to mining subsidence monitoring. Consequently, this integrated approach provides more accurate and reliable information on surface subsidence in mining areas.},
}

@article {pmid41750773,
year = {2026},
author = {Ștefârță, A and Brătoiu, MR and Rădoi, MA and Mercuț, V and Ionescu, M and Scrieciu, M and Petcu, IC and Mărășescu, PC and Amărăscu, MO and Popescu, AM and Vlăduțu, DE},
title = {Assessment of Salivary Parameters-pH, Buffering Capacity and Flow-Associated with Caries Susceptibility.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {4},
pages = {},
pmid = {41750773},
issn = {2075-4418},
abstract = {Background/Objectives: Saliva plays an essential role in maintaining the oral ecological balance, and its quantitative and qualitative characteristics may influence susceptibility to dental caries. The aim of this study was to determine susceptibility to dental caries based on the DMFT index and to establish a correlation between caries experience and salivary parameters in a group of young adults. Methods: This cross-sectional study was conducted between July and November 2025 on a sample of 87 fourth-year students from the Faculty of Dentistry in Craiova. Each participant underwent an intraoral clinical examination to determine the DMFT index. The salivary parameters assessed included unstimulated salivary flow rate, saliva consistency, salivary pH, stimulated salivary flow rate, and buffering capacity, using the GC Saliva-Check Buffer kit. Statistical analyses were performed using SPSS (Statistical Package for Social Sciences) software, version 26 (SPSS Inc., Armonk, NY, USA). Results: The mean DMFT index value for the entire sample was 8.26 ± 4.481, with higher values observed among female participants. Low salivary pH was significantly associated with higher DMFT values. Participants with low or very low buffering capacity exhibited higher DMFT values compared to those with normal capacity, indicating that a reduced ability to neutralize salivary acidity is associated with increased caries activity. Conclusions: The results indicate that salivary pH and buffering capacity are important factors in dental caries susceptibility among young adults. The integration of salivary testing into the diagnostic assessment of caries risk may contribute to personalized and effective preventive strategies.},
}

@article {pmid41749705,
year = {2026},
author = {Caragață, AV and Hnatiuc, M and Geman, O and Halunga, S and Tulbure, A and Iov, CJ},
title = {Smart Devices and Multimodal Systems for Mental Health Monitoring: From Theory to Application.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
pmid = {41749705},
issn = {2306-5354},
abstract = {Smart devices and multimodal biosignal systems, including electroencephalography (EEG/MEG), ECG-derived heart rate variability (HRV), and electromyography (EMG), increasingly supported by artificial intelligence (AI), are being explored to improve the assessment and longitudinal monitoring of mental health conditions. Despite rapid growth, the available evidence remains heterogeneous, and clinical translation is limited by variability in acquisition protocols, analytical pipelines, and validation quality. This systematic review synthesizes current applications, signal-processing approaches, and methodological limitations of biosignal-based smart systems for mental health monitoring. Methods: A PRISMA 2020-guided systematic review was conducted across PubMed/MEDLINE, Scopus, the Web of Science Core Collection, IEEE Xplore, and the ACM Digital Library for studies published between 2013 and 2026. Eligible records reported human applications of wearable/smart devices or multimodal biosignals (e.g., EEG/MEG, ECG/HRV, EMG, EDA/GSR, and sleep/activity) for the detection, monitoring, or management of mental health outcomes. The reviewed literature after predefined inclusion/exclusion criteria clustered into six themes: depression detection and monitoring (37%), stress/anxiety management (18%), post-traumatic stress disorder (PTSD)/trauma (5%), technological innovations for monitoring (25%), brain-state-dependent stimulation/interventions (3%), and socioeconomic context (7%). Across modalities, common analytical pipelines included artifact suppression, feature extraction (time/frequency/nonlinear indices such as entropy and complexity), and machine learning/deep learning models (e.g., SVM, random forests, CNNs, and transformers) for classification or prediction. However, 67% of studies involved sample sizes below 100 participants, limited ecological validity, and lacked external validation; heterogeneity in protocols and outcomes constrained comparability. Conclusions: Overall, multimodal systems demonstrate strong potential to augment conventional mental health assessment, particularly via wearable cardiac metrics and passive sensing approaches, but current evidence is dominated by proof-of-concept studies. Future work should prioritize standardized reporting, rigorous validation in diverse real-world cohorts, transparent model evaluations, and ethics-by-design principles (privacy, fairness, and clinical governance) to support translation into practice.},
}

@article {pmid41742940,
year = {2026},
author = {Mendes, L and Oliveira, J and Simões, M and Pinto, M and Castelo-Branco, M},
title = {Remote cognitive training for older adults using tablets: A pilot trial.},
journal = {Digital health},
volume = {12},
number = {},
pages = {20552076261417771},
pmid = {41742940},
issn = {2055-2076},
abstract = {BACKGROUND: Cognitive decline significantly affects the functional and intrinsic capacities of older adults, highlighting the need for effective interventions. Evidence suggests that mentally stimulating activities, particularly those supported by digital technologies, can promote cognitive health and quality of life in aging populations.

OBJECTIVE: This pilot trial examined the feasibility and preliminary effectiveness of GameAAL, a multidomain Cognitive Training programme delivered via tablet and television, in older adults with cognitive impairment or dementia.

METHODS: The intervention targeted key cognitive domains including attention, reaction time, memory, language, and executive functioning. Forty-one older adults (aged 60-93), living in nursing homes, participated in a 6-month programme. The tablet intervention group (n = 10) completed 30 sessions using a tablet device, while the TV intervention group (n = 31) completed nine sessions using a TV interface. All participants engaged with six serious games designed around cognitive tasks related to activities of daily living.

RESULTS: Pre- and post-intervention assessments included the Montreal Cognitive Assessment (MoCA) and the Hospital Anxiety and Depression Scale (HADS). The Tablet group showed a trend towards improved MoCA scores following the intervention, whereas the TV group did not show significant changes. At the post-intervention, the Tablet group demonstrated significantly better cognitive performance compared to the TV group (p = 0.044). No significant between-group differences were observed in HADS scores.

CONCLUSION: The findings suggest that the GameAAL Cognitive Training programme may help improve cognitive function in older adults with cognitive impairment by combining computer-based exercises with ecologically valid tasks.},
}

@article {pmid41741663,
year = {2026},
author = {Pankararu, CJ and Teixidor-Toneu, I and Odonne, G and Asante, F and Bandeira, SO and Barrera-Bello, ÁM and Benitez-Capistros, FJ and Dahdouh-Guebas, F and Dalcin, E and Dennehy-Carr, ZH and Diallo, K and Drouet-Cruz, HT and Fonseca-Kruel, VS and Gallois, S and Gnansounou, SC and Hamza, AJ and Hugé, J and Jordan, FM and Kalle, R and Khan, NI and Kuijper, I and Levis, C and Lima, AS and Mattalia, G and Milliken, W and Munga, CN and Narchi, NE and Ngeve, MN and Ofori, SA and Phartyal, SS and Peroni, N and Pironon, S and Polanía, J and Prakofjewa, J and Silva, MT and Sõukand, R and Thomas, MB and Ulian, T and Uprety, Y and Vandebroek, I and Ximenes, AC and Zank, S and Hanazaki, N},
title = {A global biodiversity use data infrastructure acknowledging indigenous and local knowledge.},
journal = {npj biodiversity},
volume = {5},
number = {1},
pages = {},
pmid = {41741663},
issn = {2731-4243},
abstract = {Many global biodiversity datasets overlook or misrepresent the knowledge of Indigenous Peoples, Local Communities, and Afro-Descendants (IPLCAD). We propose minimum data and metadata standards for a global data infrastructure on biodiversity knowledge and use, co-designed with IPLCAD, including information on language, community attribution and consent, to ensure data traceability and ethical use. This initiative integrates ancestral and academic sciences to advance inclusive biodiversity governance, addressing historical inequities for global sustainability.},
}

@article {pmid41741145,
year = {2026},
author = {Watanabe, F and Muramatsu, K and Tokutsu, K and Okawara, M and Fushimi, K and Matsuda, S},
title = {Functional Differentiation Among Medical Institutions During COVID-19 State of Emergency Periods: Autoregressive Integrated Moving Average Analysis of Percutaneous Coronary Intervention Using Diagnosis Procedure Combination Data.},
journal = {The Tohoku journal of experimental medicine},
volume = {},
number = {},
pages = {},
doi = {10.1620/tjem.2026.J016},
pmid = {41741145},
issn = {1349-3329},
}

@article {pmid41741097,
year = {2026},
author = {Tamm, J and Takano, K and Just, L and Ehring, T and Rosenkranz, T and , and Kopf-Beck, J},
title = {Early Improvement Predicts Treatment Response in Depression: An Ecological Momentary Assessment Study in an Inpatient and Day Clinic Setting.},
journal = {Behavior therapy},
volume = {57},
number = {2},
pages = {234-249},
doi = {10.1016/j.beth.2025.08.002},
pmid = {41741097},
issn = {1878-1888},
abstract = {Predicting treatment response through early improvement can reduce patients' time in ineffective treatments before considering alternatives. However, for psychological interventions, there is no consensus on what time window and improvement rate early in the treatment is the most informative for distinguishing treatment responders from nonresponders. This study investigated these aspects in an inpatient and day clinic setting among severe depressed patients who perceived intensive psychological treatment and compared Weekly Questionnaire Assessments (WQA) and Ecological Momentary Assessment (EMA) regarding their power to predict treatment response through early improvement. Fifty-two depressed patients were randomly assigned to one of three intensive 7-week psychological interventions (two individual and two group sessions per week) applied in an inpatient or day clinic setting. Early improvement was assessed three times daily using EMA and weekly using questionnaires (BDI-II). Linear Regression Models and Receiver Operating Characteristic Analyses were conducted to predict treatment response (BDI-II improvement from pre- to postintervention ≥50%) in patients who received a full course of treatment. Moreover, ratios of true negative/false negative predictions were calculated to explore the predictive value of different early improvement definitions: 10%, 20%, 30%, or 40% improvement after 1, 2, 3, or 4 treatment weeks. Both EMA and WQA significantly predicted treatment response after 3 weeks with AUC values of 73% (EMA) and 77% (WQA). A WQA-assessed 10% improvement after 4 weeks yielded the highest ratio of true negative/false negative predictions, with a true negative rate of 22% and a false negative rate of 0%. 10% improvement in depressive symptoms assessed with WQA after 3 to 4 weeks of treatment was the best predictor in our study. Further research is needed to validate the results. This trial design is registered with osf.io/9fuhn.},
}

@article {pmid41740147,
year = {2026},
author = {Rowland, BW and Sexton, V and Mill, A and Rushton, S and Sanderson, R and Grundy, C and de Lusignan, S and Cunliffe, NA and Hungerford, D and Hopkins, M and Gharbia, S and Jenkins, C and Godbole, G and Vivancos, R and Elliot, AJ and Mellor, DJ and Larkin, L and Chalmers, R and O'Brien, S and , },
title = {The Third Study of Infectious Intestinal Disease (IID3 Study) in the Community: Protocol for UK-Based Prospective Cohort Studies Investigating the Disease Burden.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e88759},
doi = {10.2196/88759},
pmid = {41740147},
issn = {1929-0748},
abstract = {BACKGROUND: There is a significant hidden burden of infectious intestinal disease (IID) in the UK community, which has increased over time. In the late 2000s, the Second Study of Infectious Intestinal Disease (IID2 study) estimated 17 million IID cases annually in the United Kingdom. However, only a small proportion of cases present to health care, and even those are often not tested for causative organisms.

OBJECTIVE: The Third Study of Infectious Intestinal Disease (IID3 study) aims to determine the IID burden in the UK community, estimate the underreporting level in routine practice and the general population, and recalibrate UK national surveillance based on the new incidence rates.

METHODS: We will follow methods of previous studies, along with modern pathogen detection methods and digital platforms for recruitment and follow-up. Participants will be recruited to three population-based prospective cohorts: cohort 1 (the general population), cohort 2 (patients with IID presenting to general practices [GPs]), and cohort 3 (enumeration study of IID cases presenting to GPs). Microbiological analysis of stool samples in cohorts 1 and 2 will include testing for a wide range of causative organisms using molecular assays, including pathogen targets not routinely sought by National Health Service (NHS) laboratories. Additional characterization of pathogens will be conducted at national reference laboratories. The incidence rates of IID and organisms detected in cohorts 1-3 will be compared to national surveillance systems, both laboratory and syndromic. Descriptive statistics and analysis will allow comparison of IID rates within each cohort, estimate the overall burden of disease caused by different pathogens, and compare findings to earlier IID studies.

RESULTS: A favorable ethical opinion was obtained from the UK Health Research Authority on August 4, 2022. A pilot phase to test the sampling process was conducted from January to August 2023. Participant recruitment commenced on September 1, 2023, for cohort 2 and on March 16, 2024, for cohort 1; recruitment ceased on August 31, 2025. Data collection is complete, and data analysis is to begin. The study is expected to end in September 2026.

CONCLUSIONS: Since the first and second IID studies, changes have occurred within national surveillance systems, the NHS structure, and public recommendations about when to consult a GP and where to seek health care advice, which may have altered the extent of IID reporting and the perceived burden in the community, creating greater uncertainty about the representativeness of IID rates. The IID3 study results will provide insight into trends in disease incidence over time and help quantify inequalities in IID in the UK community. Revised estimates can inform policy related to prevention, including food standards and disease management. Furthermore, advances in molecular diagnostics will significantly enhance pathogen detection, increasing our understanding of the causes of IID.

DERR1-10.2196/88759.},
}

@article {pmid41739554,
year = {2026},
author = {Echigoya, S and Ohmura, T and Sato, K and Nakagaki, T and Nishigami, Y},
title = {Geometrical preference of anchoring sites in the unicellular organism Stentor coeruleus.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {9},
pages = {e2518816123},
doi = {10.1073/pnas.2518816123},
pmid = {41739554},
issn = {1091-6490},
support = {2021-6029//Japan Science Society (JSS)/ ; None//Promotion Project for Young Investigators in Hokkaido University/ ; JPMJFS2101//Establishment of University Fellowships towards the Creation of Science Technology Innovation/ ; 2300464//Sumitomo Foundation (SF)/ ; JP21H05303//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H05308//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21H05310//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H04300//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K09388//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP24K23220//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP25K17535//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {*Ciliophora/physiology ; Hydrodynamics ; Movement/physiology ; Calcium/metabolism ; },
abstract = {Organisms often inhabit environments comprising complex structures across various scales. Animals rely on visual information from surrounding geometrical structures for navigation. Even at the microscale, various microsediments form complex structures in microbial habitats. The movement of microorganisms is passively affected by collisions and hydrodynamic interactions with surrounding structures. However, the influence of microenvironmental geometry on behavioral changes of unicellular organisms that lack visual perception remains unclear. Here, we developed geometrically structured chambers to investigate anchoring site preferences in the swimming ciliate Stentor coeruleus. Our experiments revealed that S. coeruleus preferentially anchored in narrow regions characterized by specific geometrical features, including corner angle, depth, and curvature at the corner end. Before anchoring, free-swimming S. coeruleus changed its behavior to move along the boundary wall of the chambers, accompanied by Ca[2+]-induced asymmetrical body deformation. To further investigate how S. coeruleus moves along the wall continuously, we conducted a hydrodynamic simulation and revealed that the asymmetric morphology causes asymmetric propulsive forces, explaining wall-following behavior through physical interactions with a wall. Thus, morphological change near a wall causes wall-following behavior, facilitating the identification of these narrow anchoring sites. Our findings indicate that environmental geometry drives behavioral transitions in S. coeruleus through simple biophysical processes, enabling spatial selection without visual cues. Overall, these results suggest that microgeometry plays a key role in shaping ecological niches for unicellular microorganisms.},
}

*Ciliophora/physiology
Hydrodynamics
Movement/physiology
Calcium/metabolism

@article {pmid41738306,
year = {2026},
author = {Baalsrud, HT and Tørresen, OK and Danneels, B and Ferrari, G and Tooming-Klunderud, A and Skage, M and Kollias, S and Arnyasi, M and Svensen, E and Kuklinski, P and Jakobsen, KS and Liow, LH},
title = {Chromosomal Fusions Shaped the Genome of the Greater Hornwrack Bryozoan (Flustra Foliacea) (Linnaeus, 1758).},
journal = {The Journal of heredity},
volume = {},
number = {},
pages = {},
doi = {10.1093/jhered/esag013},
pmid = {41738306},
issn = {1465-7333},
abstract = {The phylum Bryozoa is an understudied, yet commonly-occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in 8 autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores > 90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat (LTR) retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.},
}

@article {pmid41733649,
year = {2026},
author = {Liang, X and Guo, J and Lei, W and Wang, H and Fan, Q and He, S},
title = {Spatial Distribution and Environmental Risk Assessment of Neonicotinoids, Antibiotics, and Heavy Metals in the Yellow River Riparian Soils.},
journal = {Environmental management},
volume = {76},
number = {4},
pages = {},
pmid = {41733649},
issn = {1432-1009},
support = {52300244//National Natural Science Foundation of China/ ; },
mesh = {*Neonicotinoids/analysis ; *Anti-Bacterial Agents/analysis ; *Soil Pollutants/analysis ; Rivers/chemistry ; Environmental Monitoring ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; China ; Insecticides/analysis ; Water Pollutants, Chemical/analysis ; },
abstract = {Co-occurring contaminants in riparian soils posed a growing threat to the sustainable development of the Yellow River Basin. However, understanding of the co-occurrence patterns and key drivers of heavy metals (HMs), antibiotics, and neonicotinoid insecticides (NNIs) at the watershed scale remains limited. Therefore, we selected surface soil along the Yellow River to analyze its content characteristics, spatial patterns, and interrelationships. Detection rates of NNIs, antibiotics, and HMs in soils exceeded 99%. The average content of total NNIs (∑8NNIs) was 5.118 ng/g, with thiacloprid (1.667 ng/g) being the predominant component (32.5%). Total antibiotics averaged 0.412 ng/g, dominated by quinolones (47.8%) and macrolides (30.9%). The concentrations of As, Cr, and Zn among the HMs were 5.7-18.0 μg/g, 53.4-91.1 μg/g, and 35.6-94.3 μg/g, respectively, exceeding their background values at 36%, 21%, and 37% of the sampling sites, respectively. Soil organic matter content and pH negatively correlated with NNIs but positively with HMs, while fine soil particles positively correlated with both. Furthermore, ∑8NNIs (7.680 ng/g) and the contents of thirteen antibiotics (∑13ABX, 13.956 ng/g) in corn-cultivated soils were higher than in other cropped types, while ∑8NNIs (0.780 ng/g) and ∑13ABX (0.003 ng/g) in reed marshes were lower than in other cultivated soils. Health and ecological risks were generally low across the study area, but some specific sites posed potential integrated contamination risks. The study provided scientific data on the environmental fate and risks of NNIs, antibiotics, and HMs in riparian soils of large-scale watersheds, and underscored the need for more efficient usage practices and integrated watershed management strategies.},
}

*Neonicotinoids/analysis
*Anti-Bacterial Agents/analysis
*Soil Pollutants/analysis
Rivers/chemistry
Environmental Monitoring
Risk Assessment
*Metals, Heavy/analysis
Soil/chemistry
China
Insecticides/analysis
Water Pollutants, Chemical/analysis

@article {pmid41730638,
year = {2026},
author = {Okui, T and Fukushima, H and Maeda, M and Oda, F and Nakashima, N and Fukuda, H},
title = {A short-term association between hospitalizations for mental disorders and ambient temperature in Japan: an ecological study using the LIFE Study data.},
journal = {Environmental health and preventive medicine},
volume = {31},
number = {},
pages = {12},
doi = {10.1265/ehpm.25-00377},
pmid = {41730638},
issn = {1347-4715},
mesh = {Japan/epidemiology ; Humans ; *Hospitalization/statistics & numerical data ; Male ; Female ; Middle Aged ; *Mental Disorders/epidemiology/etiology ; Aged ; Adult ; *Temperature ; Young Adult ; Cities/epidemiology ; Aged, 80 and over ; Adolescent ; },
abstract = {BACKGROUND: Few studies have investigated the association between ambient temperature and the risk of mental disorders in Japan. In this study, we investigated a short-term association between the risk of hospitalizations for mental disorders and ambient temperature using municipal health insurance data.

METHODS: We used the data of the Longevity Improvement & Fair Evidence Study in Japan, and the data of 17 municipalities were employed in the analysis. The daily number of hospitalizations for schizophrenia, depressive disorders, and anxiety disorders was used as the outcome variable. The time-stratified case-crossover design was employed in this ecological time-series study, and a distributed-lag non-linear model using a conditional quasi-Poisson regression model was employed to investigate an association between ambient temperature and hospitalizations for the abovementioned mental disorders. The model was applied to each municipality, and a multivariate meta-analysis was conducted to pool the results of municipalities. In addition, subgroup analyses by sex and age groups were conducted, and temperature-related attributable fractions of the mental disorders were also calculated.

RESULTS: The results of the overall cumulative effect of ambient temperature on hospitalizations for mental disorders indicated that the risk ratio (RR) tended to increase with an increase in temperature regardless of the type of mental disorder. An analysis by sex indicated that the RR tended to increase with an increase in temperature regardless of sex. In addition, an analysis by age group indicated that an increase in RR with increasing temperature was more evident in persons aged <65 years compared to those aged ≥65 years regardless of mental disorders, and that the temperature-related attributable fractions were also higher in persons aged <65 years.

CONCLUSIONS: Higher temperatures were associated with a higher risk of hospitalization for mental disorders in Japan, while the degree of the association differed by age group.},
}

Japan/epidemiology
Humans
*Hospitalization/statistics & numerical data
Male
Female
Middle Aged
*Mental Disorders/epidemiology/etiology
Aged
Adult
*Temperature
Young Adult
Cities/epidemiology
Aged, 80 and over
Adolescent

@article {pmid41728910,
year = {2026},
author = {Liu, Y and Niu, B and Zhang, T and Wang, J and Lin, X and Zhu, L and Lv, J and Yu, R and Li, X and Zhu, J and Hu, J and Jin, LN and Chan, LL and Li, Y and Zhang, L},
title = {Environmental Drivers and Trophic Transfer of Domoic Acid in a Eutrophic Subtropical Estuary: Linking Toxigenic Pseudonitzschia Dynamics to Ecosystem Risks.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c00346},
pmid = {41728910},
issn = {1520-5851},
abstract = {Domoic acid (DA), a neurotoxin produced by certain diatoms of Pseudonitzschia, poses significant risks to marine ecosystems and human health, yet its dynamics in subtropical eutrophic estuaries remain poorly understood. This study investigates DA production and trophic transfer in the Pearl River Estuary, combining chemotaxonomy, morphological identification, ITS1 metabarcoding, and HPLC-MS/MS analysis. We revealed strong seasonal and spatial heterogeneity in Pseudonitzschia assemblages, identifying Pseudonitzschia cuspidata Clade III as a dominant DA producer with an estimated in situ cellular quota of 0.1-0.8 pg cell[-1] for the community. DA was ubiquitously detected across trophic levels, with summer maxima in phytoplankton to zooplankton, crustaceans, and mollusks, exceeding safety thresholds with 24.1 mg kg[-1] in scallops. Baseline DA contamination persisted year-round, with this chronic risk amplified by increased summer diatom biomass. Crucially, DA production was governed by optimal salinity and temperature and linked to nutrient stoichiometry rather than absolute nutrient concentration; chronic high nutrient levels showed a negative correlation with DA production. These environmental drivers also influenced DA transfer efficiency, with summer conditions amplifying contamination despite sub-bloom cell densities. These findings reveal underestimated risks in subtropical estuaries, providing a critical framework for monitoring and managing DA contamination under climate variability.},
}

@article {pmid41722362,
year = {2026},
author = {Mimura, H and Osaki, T and Takamori, S and AlSaleh, MA and Antony, B and Takeuchi, S},
title = {Cell-based biohybrid sensing of a volatile aggregation pheromone component associated with the invasive red palm weevil.},
journal = {Biosensors & bioelectronics},
volume = {302},
number = {},
pages = {118537},
doi = {10.1016/j.bios.2026.118537},
pmid = {41722362},
issn = {1873-4235},
abstract = {The red palm weevil (Rhynchophorus ferrugineus, RPW) is a highly destructive invasive pest of palm trees, causing severe agricultural and economic losses worldwide. Adult males release an aggregation pheromone, primarily (4RS,5RS)-4-methylnonan-5-ol (ferrugineol), which mediates colony formation and infestation within palm trunks. Because all life stages of this weevil are hidden inside the tree and remain undetected until fatal damage occurs, rapid and sensitive detection of pheromone emissions from the weevil colony is crucial for early detection and monitoring. However, practical sensor technologies capable of detecting this pheromone have not yet been established. Here, we report a cell-based biohybrid sensor capable of detecting pheromones in the vapor phase. This sensor employs HEK293 cells transiently co-expressing the RPW pheromone receptor RferOR1, its co-receptor RferOrco, and the genetically encoded fluorescent calcium indicator GCaMP. The specificity and sensitivity of these cells were first validated for ferrugineol in aqueous solution (0.1-10 μM), showing decreased responses at 100 μM indicative of non-monotonic behavior. The cells were then encapsulated in hydrogel matrices and integrated into a microwell array. We found that the resulting cell-based sensor exhibited a monotonic fluorescence response to ferrugineol across a broader concentration range (0.1-100 μM), likely due to moderated diffusion of ferrugineol within the hydrogel. Furthermore, the sensor successfully detected ferrugineol in the vapor phase at sub-ppm concentrations (0.1-100 ppm). These findings demonstrate that the developed sensor provides a technological basis for pheromone-detection systems for RPW monitoring, thereby extending the applicability of biohybrid sensing to ecologically relevant odorants.},
}

@article {pmid41716623,
year = {2026},
author = {Robinson, M and Letovsky, S and Liu, AH and Weber, RW and Rafalko, JM and Valcour, A},
title = {Tree pollen allergen sensitization: Prevalence, risk factors, and geographic variation in the United States.},
journal = {The journal of allergy and clinical immunology. Global},
volume = {5},
number = {3},
pages = {100642},
pmid = {41716623},
issn = {2772-8293},
abstract = {BACKGROUND: Many tree pollens are associated with the pathogenesis of allergic disease.

OBJECTIVE: Our aim was to investigate prevalence, risk factors, and geographic variation of tree pollen sensitization in the United States.

METHODS: Results of specific IgE testing for pollen of 31 tree species were obtained from a single United States-wide clinical laboratory by physicians' requests submitted in 2014-2023. Tree pollen sensitization data were statistically analyzed with respect to prevalence, patterns, and relationship with demographic characteristics, clinical diagnoses, and geographic regions.

RESULTS: A total of 23,932,544 specific IgE tests, originating from 3,067,173 unique patients ranging in age from 0 to 85 years were identified. Males showed higher positivity rates across all tree species and age groups. In both sexes, positivity was highest in individuals aged 10 to 19 years and in patients with atopic dermatitis and asthma. Patients living in urban areas had higher rates of sensitization than patients in rural areas. Considerable differences in top sensitizers were identified across ecoregions, even among different ecoregions present within the same US state. Rates of cosensitization to allergen pairs were generally associated with phylogenetic proximity of species.

CONCLUSION: Factors associated with higher rates of tree pollen sensitization included being male, being a teenager, having atopic dermatitis, having asthma, and living in a specific ecologic region. Results from this study may be helpful to clinicians in counseling patients, as well as to laboratories designing geographically based allergen testing panels.},
}

@article {pmid41715878,
year = {2026},
author = {Sun, H and Radicchi, F and Bianconi, G},
title = {Triadic percolation on multilayer networks.},
journal = {Physical review. E},
volume = {113},
number = {1-1},
pages = {014313},
doi = {10.1103/yvtg-wnn4},
pmid = {41715878},
issn = {2470-0053},
abstract = {Triadic interactions are special types of higher-order interactions that occur when regulator nodes modulate the interactions between other two or more nodes. In the presence of triadic interactions, a percolation process occurring on a single-layer network becomes a full fledged dynamical system, characterized by period doubling and a route to chaos. Here we generalize the model to multilayer networks and name it as the multilayer triadic percolation (MTP) model. We find a much richer dynamical behavior of the MTP model than its single-layer counterpart. MTP displays a Neimark-Sacker bifurcation, leading to oscillations of arbitrarily large period or pseudoperiodic oscillations. Moreover, MTP admits period-two oscillations without negative regulatory interactions, whereas single-layer systems only display discontinuous hybrid transitions. This comprehensive model offers new insights on the importance of regulatory interactions in real-world systems such as brain networks, climate, and ecological systems.},
}

@article {pmid41714061,
year = {2026},
author = {Ramesh, B and Freisthler, B and Ye, Y and Kieninger, K and Barboza-Salerno, G and Thurston, H},
title = {Relationship between time spent in outdoor recreational areas and stress among parents during the COVID-19 lockdown - A spatial temporal analysis of GPS traces from geographical EMA.},
journal = {Spatial and spatio-temporal epidemiology},
volume = {56},
number = {},
pages = {100782},
doi = {10.1016/j.sste.2026.100782},
pmid = {41714061},
issn = {1877-5853},
mesh = {Humans ; *COVID-19/epidemiology/prevention & control/psychology ; Male ; Female ; *Parents/psychology ; Adult ; Spatio-Temporal Analysis ; *Stress, Psychological/epidemiology ; *Recreation/psychology ; Geographic Information Systems ; Ecological Momentary Assessment ; Time Factors ; SARS-CoV-2 ; *Quarantine/psychology ; Middle Aged ; Parks, Recreational ; Self Report ; },
abstract = {BACKGROUND: The early COVID-19 period, with stay-at-home orders, was particularly stressful for parents. Outdoor recreation areas (ORAs), such as green spaces, may have helped alleviate stress.

AIM: To estimate the association between ORA visits and self-reported stress using geographical ecological momentary assessment (gEMA) with refined multi-sourced ORA boundaries.

METHODS: Self-reported stress was collected from a cohort of 286 participants via EMA three times daily over 14 days, alongside continuous GPS tracking. ORA visit durations were derived by spatio-temporal clustering of GPS tracks. Generalized ordinal logistic regression model supporting partial proportional odds was used to estimate the association between ORA visit duration stress, adjusting for baseline covariates and weather.

RESULTS: A minute-wise increase in ORA visit duration was not significantly associated with stress (Odds Ratio=0.99; 95% CI: 0.99 to 1.00). However, when the duration was categorized, ORA visits lasting between 15 and 35 min were associated with a 40% reduction in the odds of reporting higher stress (95% CI: 10% to 60%). A similar association was observed for shorter ORA visits (≤ 5 min), though the effect varied across stress levels. The odds of reporting higher stress were also associated with whether the parent was with their focal child, parental sex, marital status, work status, the time of day, and weekday/weekend.

CONCLUSION: Spending 15-35 min in ORAs may be optimal for parents to manage stress during challenging periods, such as the stay-at-home phase of the COVID-19 pandemic. Even brief ORA visits (< 5 min) may help parents experiencing high stress.},
}

Humans
*COVID-19/epidemiology/prevention & control/psychology
Male
Female
*Parents/psychology
Adult
Spatio-Temporal Analysis
*Stress, Psychological/epidemiology
*Recreation/psychology
Geographic Information Systems
Ecological Momentary Assessment
Time Factors
SARS-CoV-2
*Quarantine/psychology
Middle Aged
Parks, Recreational
Self Report

@article {pmid41713447,
year = {2026},
author = {Song, P and Jiang, D and Zhou, J and Zhu, Y and Manaf, RA and Bojude, DA and Agbre-Yace, ML and Ali, S and Allen, O and Anyasodor, AE and Aranda, Z and Bahattab, A and Bodomo, A and Borrescio-Higa, F and Buchtova, M and Buljan, N and Deshmukh, V and Díaz-Castro, L and Cheema, S and Ekezie, W and Ganasegeran, K and Ganesan, B and Glasnović, A and Graham, CJ and Htay, MNN and Igwesi-Chidobe, C and Iversen, PO and Islam, MM and Karim, AJ and Kalpič, B and Kanma-Okafor, O and Lanza, G and Luz, S and Mahikul, W and Mladenić, D and Manyara, AM and Munipalli, B and Myburgh, N and Ng, ZX and Nikolopoulos, G and Park, C and Park, JJ and Peprah, P and Rudan, K and Shah, SA and Shi, T and Tiglic, GŠ and Sutan, R and Tsanas, A and Tibble, H and Khpalwak, AT and Tomlinson, M and Vento, S and Glasnović, JV and Wang, L and Xu, J and Zhang, J and Zhang, Y and Sheikh, E and Ozoh, OB and Tsiachristas, A and Adeloye, D and Kerr, S and Sanwalka, M and Orešković, S and Sheikh, A and Rudan, I},
title = {Research priorities for data science and artificial intelligence in global health: an international consensus exercise.},
journal = {The Lancet. Global health},
volume = {14},
number = {3},
pages = {e455-e465},
doi = {10.1016/S2214-109X(25)00473-5},
pmid = {41713447},
issn = {2214-109X},
mesh = {Humans ; *Artificial Intelligence ; *Global Health ; *Data Science ; Consensus ; *Research ; Developing Countries ; },
abstract = {Applications of data science and artificial intelligence (AI) in global health are expanding, yet research remains fragmented and often misaligned with the needs of low-income and middle-income countries (LMICs). To address this misalignment, we conducted a global research priority-setting exercise using the Child Health and Nutrition Research Initiative (CHNRI) method. 155 research ideas were scored by 51 experts based on feasibility, potential impact on disease burden, paradigm shift potential, implementation potential, and equity. Top-ranked priorities focused on epidemic preparedness, including AI-based outbreak prediction, improved diagnostics for infectious diseases, and early-warning systems. Other highly ranked topics included AI-assisted resource allocation, telemedicine, culturally adapted mobile health services, and chronic disease management tools. Experts from LMICs prioritised infectious disease control and diagnostic equity, whereas experts from high-income countries emphasised infrastructure and climate-related analytics. The resulting agenda provides a roadmap for aligning AI and data science research with global health priorities, particularly in LMICs.},
}

Humans
*Artificial Intelligence
*Global Health
*Data Science
Consensus
*Research
Developing Countries

@article {pmid41712942,
year = {2026},
author = {Thompson, DA and Kaizer, LK and Schmiege, SJ and Cabrera, NJ and Clark, L and Ringwood, H and Miramontes Valdes, E and Jimenez-Zambrano, A and Gorman, C and Babiak, M and Tschann, JM},
title = {Maternal Screen-Related Behaviors, Toddler Screen Use, and Toddler BMI in Mexican American Families: Cross-Sectional Study.},
journal = {JMIR pediatrics and parenting},
volume = {9},
number = {},
pages = {e76873},
pmid = {41712942},
issn = {2561-6722},
abstract = {BACKGROUND: Parents, as the most proximal influence on young children, play an important role in shaping toddler behaviors. Yet, evidence on how parents shape toddler screen use is limited. Little is also known about the relationship between toddler screen use and BMI. Given existing disparities in screen use and early childhood obesity, a focus on Mexican American families with toddlers is warranted.

OBJECTIVE: This study aimed to evaluate the independent contributions of both maternal screen use and screen-related parenting practices with toddler screen use duration, for both TV viewing and mobile device use, and examine the relationship between toddler screen use duration and BMI.

METHODS: This cross-sectional study enrolled 384 Mexican American mother-toddler dyads recruited from safety net clinics. Enrolled mothers completed 7-day screen use diaries and surveys on screen-related parenting practices, and toddler anthropometrics were obtained. Negative binomial regression models estimated the relationships between screen-related parenting practices and maternal screen use (predictors) with child duration of daily TV use and mobile device use (outcomes). Spearman correlations were calculated to estimate the relationship between toddler screen use duration and age- and sex-specific BMI z scores.

RESULTS: Maternal duration of daily TV and mobile device use were associated with toddler duration of daily TV (adjusted rate ratios [aRRs] 1.27-1.28; all P<.001) and mobile device use (aRRs 1.17-1.18; all P<.001), respectively, even after adjusting for maternal screen-related parenting practices. Specific parenting practices, including restriction of TV time (aRR=0.86; P=.01), restriction of mobile device time (aRR=0.80; P=.02), use of TV (aRR=1.27; P=.003) and mobile devices (aRR=1.78; P<.001) for child behavior regulation, and coviewing of mobile devices (aRR=1.51; P<.001), were associated with toddler duration of daily screen use, adjusted for maternal duration of daily screen use. Neither toddler duration of daily TV viewing nor daily mobile device use was correlated with toddler BMI z scores.

CONCLUSIONS: Both the duration of maternal screen use and screen-related parenting practices, for both TV and mobile devices, should be considered when promoting healthy screen use in toddlers in Mexican American families. Interventionists should consider the family ecology when designing interventions promoting healthy screen use in early childhood.},
}

@article {pmid41707187,
year = {2026},
author = {Kong, J and Bragazzi, NL},
title = {Framing the Convergence of One Health and Digital Health in the Global South With a Gender-Sensitive Foresight Perspective: Delphi Study Using Latent Semantic Analysis.},
journal = {Journal of medical Internet research},
volume = {28},
number = {},
pages = {e78702},
doi = {10.2196/78702},
pmid = {41707187},
issn = {1438-8871},
mesh = {Delphi Technique ; Humans ; Female ; *Global Health ; Male ; Semantics ; Artificial Intelligence ; Sex Factors ; *Digital Technology ; Digital Health ; },
abstract = {BACKGROUND: The convergence of digital health and One Health represents an emergent paradigm in global health governance. While widely discussed in high-income settings, there is limited understanding of how this convergence is conceptualized in the Global South, particularly when viewed through a gender- and equity-sensitive foresight lens.

OBJECTIVE: This study aimed to map and classify expert discourse on digital health, One Health, and their convergence in the Global South using latent semantic analysis, with particular attention to structural drivers, emerging issues, weak signals, and gendered patterns of anticipation.

METHODS: A 3-round online Delphi survey was conducted with 45 experts from 19 countries across the Global South. Open-ended responses were analyzed using latent semantic analysis and stratified by gender. A foresight framework was applied to categorize topics as structural drivers, emerging issues, or weak signals, based on their temporal persistence, salience, and consensus.

RESULTS: In digital health, structural drivers included the systemic integration of digital technologies into public health systems, strategic alignment, and infrastructure development. Emerging issues comprised the adoption of artificial intelligence, chronic disease management via mobile health, and concerns about digital inclusion and interoperability. Weak signals included feminist digital ethics, trust in digital systems, and relational accountability-more frequently emphasized by female experts. In One Health, structural drivers were centered on intersectoral coordination, ecological integration, and the institutionalization of health-environment frameworks. Emerging issues encompassed anticipatory risk governance, food system sustainability, and the integration of environmental and population-level data. Weak signals included indigenous knowledge systems, subnational antimicrobial resistance governance, and structural underinvestment in ecological public health, with gendered divergence in framing. In the convergence discourse (digital health and One Health), structural drivers focused on the integration of digital surveillance systems, data infrastructures, and health information platforms to operationalize One Health. Emerging issues included climate-triggered system redesign, artificial intelligence and ecological monitoring, and the governance of cross-sectoral data. Weak signals pointed to algorithmic bias in zoonotic prediction, digital sovereignty in environmental health, and feminist critiques of convergence-all thematically rich but peripheral in consensus.

CONCLUSIONS: This study revealed a multilayered and gender-influenced foresight architecture shaping the future of digital health and One Health in the Global South. Structural drivers denote maturing domains of implementation, while emerging issues and weak signals highlight latent, often overlooked opportunities and tensions. Incorporating equity-sensitive and gender-aware foresight methods is essential for crafting inclusive and anticipatory health governance strategies.},
}

Delphi Technique
Humans
Female
*Global Health
Male
Semantics
Artificial Intelligence
Sex Factors
*Digital Technology
Digital Health

@article {pmid41706338,
year = {2026},
author = {Semwal, P and Majhi, B and Shivhare, R and Mishra, SK and Misra, S and Chauhan, PS},
title = {Harnessing endophytes and Multi-Omics for sustainable Colchicine biosynthesis.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {92},
pmid = {41706338},
issn = {1573-0972},
support = {OLP116//CSIR/ ; },
mesh = {*Colchicine/biosynthesis ; *Endophytes/metabolism/genetics ; Metabolic Engineering ; Metabolomics/methods ; Proteomics ; Biosynthetic Pathways ; Metabolic Networks and Pathways ; Multiomics ; },
abstract = {Gloriosa superba, an endangered medicinal plant, serves as the principal natural source of colchicine, a vital alkaloid used for treating gout, arthritis, cancer, and various inflammatory disorders. However, its conventional extraction from plant tissues is constrained by low yield, ecological degradation, and conservation concerns, necessitating sustainable production alternatives. Emerging evidence indicates that colchicine biosynthesis is not solely plant-autonomous but is strongly influenced by endophytic microorganisms that function as active metabolic partners. Endophytic fungi and bacteria associated with G. superba enhance colchicine accumulation through elicitor-mediated signaling, transcriptional reprogramming, metabolic complementation, and modulation of pathway flux. This review presents a systems-level synthesis that integrates endophyte biology with multi-omics technologies and synthetic biology to redefine colchicine biosynthesis as a coordinated plant-microbe metabolic network. Integrated transcriptomic, proteomic, and metabolomic analyses have enabled mechanistic resolution of the colchicine pathway, including identification of key enzymes, regulatory nodes, and bottlenecks such as the cytochrome P450-mediated oxidative ring expansion central to tropolone alkaloid formation. These insights underpin rational metabolic engineering, CRISPR-based genome editing, and synthetic pathway reconstruction in heterologous microbial hosts. By explicitly linking mechanistic understanding with pathway engineering and biomanufacturing design, this review advances a coherent framework for eco-efficient, scalable colchicine production while supporting conservation of G. superba.},
}

*Colchicine/biosynthesis
*Endophytes/metabolism/genetics
Metabolic Engineering
Metabolomics/methods
Proteomics
Biosynthetic Pathways
Metabolic Networks and Pathways
Multiomics

@article {pmid41705859,
year = {2026},
author = {Medeiros, WB and Centurion, VB and Silva, JB and Duarte, AW and Hidalgo-Martinez, KJ and Dos Santos, JA and Penna, DDPS and Bagci, C and Ziemert, N and Oliveira, VM},
title = {Antarctic soil prokaryotic diversity: a dataset of 319 metagenome-assembled genomes from Deception and Livingston Islands.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0134625},
doi = {10.1128/mra.01346-25},
pmid = {41705859},
issn = {2576-098X},
abstract = {A total of 319 bacterial metagenome-assembled genomes (MAGs) were recovered from soil samples collected on the Antarctic Peninsula (Deception and Livingston Islands). These MAGs reveal microbial life's phylogenetic diversity and functional potential in extreme polar environments, providing resources for advancing microbial ecology, evolution, and Antarctic biotechnology.},
}